90 research outputs found
Benthic and Planktic Foraminifera as Indicators of Late Glacial to Holocene Paleoclimatic Changes in a Marginal Environment: An Example from the Southeastern Bay of Biscay
Benthic and planktic foraminiferal assemblages from two sediment cores (2000 m depth, 44°33âČN-2°45âČW) were analyzed to first compare modern and dead faunas and next to study changes in the hydrology of the southeastern Bay of Biscay (SE BoB) over the last 12.8 cal ka BP. Considering benthic ecosystem characteristics, the first part of the paleorecord (12.8â7.6 cal ka BP) is composed of laminated sediments that may have resulted from turbiditic overflow events, whereas occurrences of transported species (e.g. Nonionella sp., Cassidulina carinata) attest of continental influence at the core location. After 7.6 cal ka BP, the sediment becomes bioturbated concomitantly to the stabilization of the sea-level. The benthic foraminiferal fauna is largely dominated by Uvigerina peregrina suggesting a high seasonality with seasonal pulsed organic matter fluxes to the seafloor. On the other hand, the planktic foraminiferal composition indicates that surface water masses were under the influence of the polar front in the early record, which retreated at about 11.5 cal ka BP. The early Holocene is characterized by relatively warm and stratified water masses at 8.4â4.8 cal ka BP. The last 4.8 cal ka BP records a gradual sea surface water cooling trend and enhanced foraminiferal production from ~2.6 cal ka BP until present. The early (12.8â10.5 cal ka BP) and late (2.3â1.7 cal ka BP) Holocene are characterized by the presence of the planktic species Globigerinoides ruber probably caused by intrusions of the Iberian Poleward Current (IPC), and a negative state of the North Atlantic Oscillation (NAO)
DynACof, a model fro growth, yield, carbon, water, energy balances and ecosystem services of Coffea in agroforestry
Agroforestry systems (AFS) are complex to model mainly due to the high spatial variability induced by the shade trees. Recently, the microclimate and lighf heterogeneity issue in AFS has been addressed using the 30 ecophysiological process-based model MAESPA (Charbonnier et al., 2013; Vezy et al., 2018). MAESPA surpassed the classical sun/shade dichotomy in AFS (Charbonnier et al., 2014) and provided continuous maps of e.g. available light, light-use~ fficiency and canopy temperature within Coffea Agroforestry Systems (GAS). A step further was to design a crop model for Coffea grown under agroforestry that would benefit from this continuum to estimate ecosystem services on the long term and under climate change scenarios. We designed DynA_Cof, a new process-based growth and yield model to compute plot-scale net and gross primary productivity, carbon allocation, growth, yield, energy, and water balance of GAS according to shade tree species and management, while accounting for fine-scale spatial effects using MAESPA metamodels (Figure 1). DynA_Cof satisfactorily simulated the daily plot-scale gross primary productivity (RMSE= 1.69 gc m-2 d-1 on 1562 days) and the energy and water balances (RMSE: AET = 0.63 mm d-1 , H= 1.27 MJ m-2 d-1, Rn= 1.98 MJ m-2 d-1) compared to measurements from an eddy-flux tower in Aquiares (Costa Rica) and also the NPP for above and below-ground organs, coffee bean yield and shade tree wood production compared to a comprehensive database from this site
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaAâK) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaEâmRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved Cârich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism
Common variants in Alzheimerâs disease and risk stratification by polygenic risk scores
Funder: Funder: FundaciĂłn bancaria âLa Caixaâ Number: LCF/PR/PR16/51110003 Funder: Grifols SA Number: LCF/PR/PR16/51110003 Funder: European Union/EFPIA Innovative Medicines Initiative Joint Number: 115975 Funder: JPco-fuND FP-829-029 Number: 733051061Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery nâ=â409,435 and validation size nâ=â58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE É4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease
New insights into the genetic etiology of Alzheimer's disease and related dementias
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE Δ4 allele
New insights into the genetic etiology of Alzheimer's disease and related dementias
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE Δ4 allele
Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimerâs disease
Alzheimerâs disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individualsâ16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-ÎČ precursor protein processing, amyloid-ÎČ aggregation, lipid metabolism and microglial function in AD
Multiancestry analysis of the HLA locus in Alzheimerâs and Parkinsonâs diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes
Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinsonâs disease (PD) and Alzheimerâs disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased AÎČ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues
BiogĂ©ochimie et hydrologie dâune plage battue : la plage du Truc Vert : flux de matiĂšre dans les sĂ©diments sableux intertidaux
Biogeochemical studies in permeable sandy sediments are recent: the role of these environments in biogeochemical cycles was neglected because of their poverty in organic matter and the complexity of transient processes affecting them. Sandy beaches are subject to various physical forcings like tide, waves and connexion with continental groundwaters. Advection is the leading mode of transport. Huge volumes of organic matter-bearing seawater are potentially filtered by permeable intertidal sediments. The main objective of this study was to characterize biogeochemical processes induced by seawater recirculation and groundwater discharge in the intertidal zone of an exposed beach: the Truc Vert beach.Seasonal monitoring of pore water properties showed that aerobic respiration processes occurred in the seawater recirculation plume. Extrapolated to the 240 km-long Aquitanian coast, these processes represent each year an annual release of 610 tons of nitrate and 4400 tons of dissolved inorganic carbon, i.e. the equivalent of the Leyre input, a small river draining a catchment area of 2000 km2 at the southeast part of the Arcachon lagoon.The benthic macrofauna is dominated by Crustaceans. These organisms have a low impact on biogeochemical cycles: the contribution of benthic macrofauna on oxygen deficits observed in the lower beach pore waters is insignificant (< 2%). Biogeochemical fluxes observed in the intertidal zone are mainly induced by the aerobic respiration of microorganisms living in the sediment. Supported by regular tidal inputs of dissolved oxygen on the pore space, these processes varied seasonnally with temperature and organic matter availability.The deployment of autonomous probes into the sediment of the intertidal zone allowed us to clarify the short-term variability of pore water properties. Extension of the intertidal saline plume evolved with the tidal amplitude. Oxygen levels measured at a given point of the beach varied slightly with the lunar cycle. This work showed that aerobic respiration processes varied mainly at the seasonal scale. The local impact of weather and swell was also evidenced.We showed the presence of a subterranean estuary in the Truc Vert beach and its dynamics was explored through the deployment of wells in the upper beach. The input of continental freshwater represents an additional source of nitrate and dissolved inorganic carbon in the coastal ocean. Chemical properties of the fresh groundwater located upstream the beach indicated a decoupling between the salinity gradient and the redox bareer within the subterranean estuary, as well as an intense CO2 degassing at the dune.This study allows to better understand the processes occuring in sandy sediments of exposed beaches and will allow to develop complex numerical models linking hydrological and biogeochemical processes. This work also provides many perspectives on the role of sandy beaches, both locally (in case of pollution, for example) and on global biogeochemical cycles, especially in relation to global warming and sea-level rise (CO2 emissions and seawater intrusion in coastal aquifers).LâĂ©tude biogĂ©ochimique des sĂ©diments sableux permĂ©ables est un domaine nouveau : le rĂŽle de ces environnements dans les cycles biogĂ©ochimiques a longtemps Ă©tĂ© nĂ©gligĂ© en raison de leur pauvretĂ© en matiĂšre organique et de la complexitĂ© des processus transitoires sây dĂ©roulant. Les plages sableuses sont en effet soumises Ă de nombreux forçages physiques, dont la marĂ©e, la houle et la connexion avec lâaquifĂšre continental. Le processus dâadvection y est le mode de transport dominant. De grands volumes dâeau de mer chargĂ©e en matiĂšre organique sont plus ou moins filtrĂ©s par les sĂ©diments permĂ©ables intertidaux. Le principal objectif de cette thĂšse Ă©tait de caractĂ©riser les processus biogĂ©ochimiques induits par la recirculation de lâeau de mer et les apports dâeau douce dans la zone intertidale dans le cas dâune plage soumise Ă de fortes conditions hydrodynamiques : la plage du Truc Vert. Un suivi saisonnier des propriĂ©tĂ©s physico-chimiques des eaux porales a montrĂ© que les processus de respiration aĂ©robie interviennent en zone intertidale, dans la lentille de recirculation de lâeau de mer. A lâĂ©chelle du littoral aquitain, ces processus reprĂ©sentent un apport annuel de 610 tonnes de nitrate et de 4400 tonnes de carbone inorganique dissous pour lâocĂ©an cĂŽtier, soit lâĂ©quivalent des apports de la Leyre, un petit fleuve drainant un bassin versant de 2000 km2 au sud-est du Bassin dâArcachon. La macrofaune benthique est dominĂ©e par les CrustacĂ©s. Ces individus sont caractĂ©ristiques de ces milieux complexes, quâils subissent mais ne contrĂŽlent pas : la macrofaune benthique contribue faiblement aux processus de respiration aĂ©robie. Seuls 2% du dĂ©ficit en oxygĂšne des eaux porales du bas de plage leur est attribuĂ© en moyenne : les flux biogĂ©ochimiques observĂ©s en zone intertidale sont donc majoritairement induits par les processus de respiration aĂ©robie des micro-organismes prĂ©sents dans le sĂ©diment. Soutenus par lâapport rĂ©gulier dâoxygĂšne dissous dans le milieu poral Ă chaque marĂ©e, ces processus sont Ă©galement contrĂŽlĂ©s par la tempĂ©rature et la variabilitĂ© des apports de matiĂšre organique.Le dĂ©ploiement de sondes autonomes dans le sĂ©diment de la zone intertidale a Ă©galement permis de prĂ©ciser la variabilitĂ© Ă court terme des propriĂ©tĂ©s des eaux porales. Lâextension de la lentille intertidale de recirculation de lâeau de mer est ainsi variable en fonction du marnage et les teneurs en oxygĂšne mesurĂ©es en un point fixe de la plage varient lĂ©gĂšrement en fonction de ce cycle. Ce travail a donc permis de dĂ©montrer que les processus de respiration aĂ©robie varient principalement Ă lâĂ©chelle saisonniĂšre. Lâimpact ponctuel et local des conditions mĂ©tĂ©orologiques et de la houle a Ă©galement Ă©tĂ© mis en Ă©vidence. Nous avons dĂ©montrĂ© lâexistence dâun estuaire souterrain sous la plage du Truc Vert. La dynamique de ce systĂšme a Ă©tĂ© explorĂ©e grĂące Ă lâinstallation de piĂ©zomĂštres en haut de plage. Lâapport dâeaux douces continentales reprĂ©sente une source supplĂ©mentaire de nitrate et de carbone inorganique dissous pour lâocĂ©an cĂŽtier. LâĂ©tude biogĂ©ochimique de la nappe phrĂ©atique en arriĂšre dune indique lâexistence dâun dĂ©couplage entre le front salin et le front redox au sein de lâestuaire souterrain, ainsi que lâexistence dâun intense dĂ©gazage de CO2 au niveau de la dune.Les travaux rĂ©alisĂ©s durant cette thĂšse permettent de mieux comprendre les processus Ă lâĆuvre dans les sĂ©diments sableux des plages exposĂ©es et permettront ainsi le dĂ©veloppement de modĂšles numĂ©riques complexes liant hydrologie et biogĂ©ochimie. Ils entraĂźnent Ă©galement de nombreuses perspectives Ă propos du rĂŽle des plages sableuses Ă lâĂ©chelle locale (en cas de pollution par exemple) mais aussi sur les cycles biogĂ©ochimiques globaux, notamment en lien avec le rĂ©chauffement climatique et lâĂ©lĂ©vation du niveau marin (rejets de CO2, salinisation des aquifĂšres cĂŽtiers)
Biogeochemistry and hydrology of a high-energy sandy beach : the Truc Vert beach : matter fluxes in intertidal sandy sediments
LâĂ©tude biogĂ©ochimique des sĂ©diments sableux permĂ©ables est un domaine nouveau : le rĂŽle de ces environnements dans les cycles biogĂ©ochimiques a longtemps Ă©tĂ© nĂ©gligĂ© en raison de leur pauvretĂ© en matiĂšre organique et de la complexitĂ© des processus transitoires sây dĂ©roulant. Les plages sableuses sont en effet soumises Ă de nombreux forçages physiques, dont la marĂ©e, la houle et la connexion avec lâaquifĂšre continental. Le processus dâadvection y est le mode de transport dominant. De grands volumes dâeau de mer chargĂ©e en matiĂšre organique sont plus ou moins filtrĂ©s par les sĂ©diments permĂ©ables intertidaux. Le principal objectif de cette thĂšse Ă©tait de caractĂ©riser les processus biogĂ©ochimiques induits par la recirculation de lâeau de mer et les apports dâeau douce dans la zone intertidale dans le cas dâune plage soumise Ă de fortes conditions hydrodynamiques : la plage du Truc Vert. Un suivi saisonnier des propriĂ©tĂ©s physico-chimiques des eaux porales a montrĂ© que les processus de respiration aĂ©robie interviennent en zone intertidale, dans la lentille de recirculation de lâeau de mer. A lâĂ©chelle du littoral aquitain, ces processus reprĂ©sentent un apport annuel de 610 tonnes de nitrate et de 4400 tonnes de carbone inorganique dissous pour lâocĂ©an cĂŽtier, soit lâĂ©quivalent des apports de la Leyre, un petit fleuve drainant un bassin versant de 2000 km2 au sud-est du Bassin dâArcachon. La macrofaune benthique est dominĂ©e par les CrustacĂ©s. Ces individus sont caractĂ©ristiques de ces milieux complexes, quâils subissent mais ne contrĂŽlent pas : la macrofaune benthique contribue faiblement aux processus de respiration aĂ©robie. Seuls 2% du dĂ©ficit en oxygĂšne des eaux porales du bas de plage leur est attribuĂ© en moyenne : les flux biogĂ©ochimiques observĂ©s en zone intertidale sont donc majoritairement induits par les processus de respiration aĂ©robie des micro-organismes prĂ©sents dans le sĂ©diment. Soutenus par lâapport rĂ©gulier dâoxygĂšne dissous dans le milieu poral Ă chaque marĂ©e, ces processus sont Ă©galement contrĂŽlĂ©s par la tempĂ©rature et la variabilitĂ© des apports de matiĂšre organique.Le dĂ©ploiement de sondes autonomes dans le sĂ©diment de la zone intertidale a Ă©galement permis de prĂ©ciser la variabilitĂ© Ă court terme des propriĂ©tĂ©s des eaux porales. Lâextension de la lentille intertidale de recirculation de lâeau de mer est ainsi variable en fonction du marnage et les teneurs en oxygĂšne mesurĂ©es en un point fixe de la plage varient lĂ©gĂšrement en fonction de ce cycle. Ce travail a donc permis de dĂ©montrer que les processus de respiration aĂ©robie varient principalement Ă lâĂ©chelle saisonniĂšre. Lâimpact ponctuel et local des conditions mĂ©tĂ©orologiques et de la houle a Ă©galement Ă©tĂ© mis en Ă©vidence. Nous avons dĂ©montrĂ© lâexistence dâun estuaire souterrain sous la plage du Truc Vert. La dynamique de ce systĂšme a Ă©tĂ© explorĂ©e grĂące Ă lâinstallation de piĂ©zomĂštres en haut de plage. Lâapport dâeaux douces continentales reprĂ©sente une source supplĂ©mentaire de nitrate et de carbone inorganique dissous pour lâocĂ©an cĂŽtier. LâĂ©tude biogĂ©ochimique de la nappe phrĂ©atique en arriĂšre dune indique lâexistence dâun dĂ©couplage entre le front salin et le front redox au sein de lâestuaire souterrain, ainsi que lâexistence dâun intense dĂ©gazage de CO2 au niveau de la dune.Les travaux rĂ©alisĂ©s durant cette thĂšse permettent de mieux comprendre les processus Ă lâĆuvre dans les sĂ©diments sableux des plages exposĂ©es et permettront ainsi le dĂ©veloppement de modĂšles numĂ©riques complexes liant hydrologie et biogĂ©ochimie. Ils entraĂźnent Ă©galement de nombreuses perspectives Ă propos du rĂŽle des plages sableuses Ă lâĂ©chelle locale (en cas de pollution par exemple) mais aussi sur les cycles biogĂ©ochimiques globaux, notamment en lien avec le rĂ©chauffement climatique et lâĂ©lĂ©vation du niveau marin (rejets de CO2, salinisation des aquifĂšres cĂŽtiers).Biogeochemical studies in permeable sandy sediments are recent: the role of these environments in biogeochemical cycles was neglected because of their poverty in organic matter and the complexity of transient processes affecting them. Sandy beaches are subject to various physical forcings like tide, waves and connexion with continental groundwaters. Advection is the leading mode of transport. Huge volumes of organic matter-bearing seawater are potentially filtered by permeable intertidal sediments. The main objective of this study was to characterize biogeochemical processes induced by seawater recirculation and groundwater discharge in the intertidal zone of an exposed beach: the Truc Vert beach.Seasonal monitoring of pore water properties showed that aerobic respiration processes occurred in the seawater recirculation plume. Extrapolated to the 240 km-long Aquitanian coast, these processes represent each year an annual release of 610 tons of nitrate and 4400 tons of dissolved inorganic carbon, i.e. the equivalent of the Leyre input, a small river draining a catchment area of 2000 km2 at the southeast part of the Arcachon lagoon.The benthic macrofauna is dominated by Crustaceans. These organisms have a low impact on biogeochemical cycles: the contribution of benthic macrofauna on oxygen deficits observed in the lower beach pore waters is insignificant (< 2%). Biogeochemical fluxes observed in the intertidal zone are mainly induced by the aerobic respiration of microorganisms living in the sediment. Supported by regular tidal inputs of dissolved oxygen on the pore space, these processes varied seasonnally with temperature and organic matter availability.The deployment of autonomous probes into the sediment of the intertidal zone allowed us to clarify the short-term variability of pore water properties. Extension of the intertidal saline plume evolved with the tidal amplitude. Oxygen levels measured at a given point of the beach varied slightly with the lunar cycle. This work showed that aerobic respiration processes varied mainly at the seasonal scale. The local impact of weather and swell was also evidenced.We showed the presence of a subterranean estuary in the Truc Vert beach and its dynamics was explored through the deployment of wells in the upper beach. The input of continental freshwater represents an additional source of nitrate and dissolved inorganic carbon in the coastal ocean. Chemical properties of the fresh groundwater located upstream the beach indicated a decoupling between the salinity gradient and the redox bareer within the subterranean estuary, as well as an intense CO2 degassing at the dune.This study allows to better understand the processes occuring in sandy sediments of exposed beaches and will allow to develop complex numerical models linking hydrological and biogeochemical processes. This work also provides many perspectives on the role of sandy beaches, both locally (in case of pollution, for example) and on global biogeochemical cycles, especially in relation to global warming and sea-level rise (CO2 emissions and seawater intrusion in coastal aquifers)
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