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Antibody–antigen complexes challenge our understanding, as analyses to date failed to unveil the key determinants of binding affinity and interaction specificity. We partially fill this gap based on novel quantitative analyses using two standardized databases, the IMGT/3Dstructure-DB and the structure affinity benchmark. First, we introduce a statistical analysis of interfaces which enables the classification of ligand types (protein, peptide, and chemical; cross-validated classification error of 9.6%) and yield binding affinity predictions of unprecedented accuracy (median absolute error of 0.878 kcal/mol). Second, we exploit the contributions made by CDRs in terms of position at the interface and atomic packing properties to show that in general, VH CDR3 and VL CDR3 make dominant contributions to the binding affinity, a fact also shown to be consistent with the enthalpy–entropy compensation associated with preconfiguration of CDR3. Our work suggests that the affinity prediction problem could be partially solved from databases of high resolution crystal structures of complexes with known affinity.

Based on a workshop organised by the Atlantic Salmon Trust, held in Edinburgh Tuesday, 6th November – Thursday, 8th November 2017. International audience

The cold-water coral Lophelia pertusa is one of the few species able to build reef-like structures and a 3-dimensional coral framework in the deep oceans. Furthermore, deep cold-water coral bioherms may be among the first marine ecosystems to be affected by ocean acidification. Colonies of L. pertusa were collected during a cruise in 2006 to cold-water coral bioherms of the Mingulay reef complex (Hebrides, North Atlantic). Shortly after sample collection onboard these corals were labelled with calcium-45. The same experimental approach was used to assess calcification rates and how those changed due to reduced pH during a cruise to the Skagerrak (North Sea) in 2007. The highest calcification rates were found in youngest polyps with up to 1% d−1 new skeletal growth and average rates of 0.11±0.02% d−1±S.E.). Lowering pH by 0.15 and 0.3 units relative to the ambient level resulted in calcification being reduced by 30 and 56%. Lower pH reduced calcification more in fast growing, young polyps (59% reduction) than in older polyps (40% reduction). Thus skeletal growth of young and fast calcifying corallites suffered more from ocean acidification. Nevertheless, L. pertusa exhibited positive net calcification (as measured by 45Ca incorporation) even at an aragonite saturation state (Ωa) below 1.

Broadband acoustic signals around 1 kHz propagate through shallow water oceanic waveguides of ~100 m in depth and ~2 km in range as multiple ray-like wavefronts. These acoustic arrivals can be characterized by the following observables: travel-time (TT), direction-of-arrival (DOA) and direction-of-departure (DOD). By applying double-beamforming on the point-to-point signals recorded between two source-receiver arrays, the acoustic contribution of each arrival can be separated from the multi-reverberated data and the TT, DOA and DOD observable variations are accurately measured. This study deals with the use of time-angle sensitivity kernels (TASK) to estimate the observable variations induced by sound speed perturbations in the waveguide. This approach is based on the first order Born approximation and takes into account the finite-frequency effects associated with wave propagation. The robustness the TASK approach is analyzed and compared to numerical parabolic equation simulations involving different sound speed perturbations. For example, parameters such as the perturbation location, the value and shape of the perturbation in the waveguide are modified. The combination of several perturbations and the influence of the source-receiver array apertures on the TT, DOA and DOD estimates are also studied.

The perception of ocean areas by policy-makers or by people, living or not on the coast, has significantly varied over centuries. Due to its vastness and complexity, the sea has been studied within distinct academic disciplines. However, the current issues related to the sea, such as climate change, marine pollution or coastal tourism, require an integrated vision of the assets and drawbacks in order to meet the challenges arising from human activities both at sea and onshore. In this study, a group of foresight officers from the French network of public research institutes decided to cross-check and compare several science approaches (biology, sociology, economics, etc) about oceans. Thus, 11 sectors of maritime activity (transportation, fisheries, energy, etc.) were cross-tabulated with 9 basic social functions (providing food, housing, learning, etc.). In this matrix, the main challenges and issues projected for 2030 were sought, in the frame of a baseline scenario. Results were clustered through 4 criteria, leading to 9 major challenges, each of them broken down into two important issues for research. The outcomes were used to create a survey, allowing the ranking of the research priorities. Most of the 9 challenges tally with the research and development objectives of great maritime states, except for governance and monitoring, which remain underscored. As a result, maritime powers still show more interest on securing national resources rather than on promoting international cooperation for secure trade and sustainable exploitation of marine resources. But foresight in this field could help changing the mentalities notably because oceans show clearly now to be a vital common good for mankind.

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

We develop and implement a new method to take into account the impact of waves into the 3-D circulation model SYMPHONIE (Marsaleix et al., 2008, 2009a) following the simplified equations of Bennis et al. (2011) which use glm2z-RANS theory (Ardhuin et al., 2008c). These adiabatic equations are completed by additional parameterizations of wave breaking, bottom friction and wave-enhanced vertical mixing, making the forcing valid from the surf zone through to the open ocean. The wave forcing is performed by wave generation and propagation models WAVEWATCH III® (Tolman, 2008, 2009; Ardhuin et al., 2010) and SWAN (Booij et al., 1999). The model is tested and compared with other models for a plane beach test case, previously tested by Haas and Warner (2009)and Uchiyama et al. (2010). A comparison is also made with the laboratory measurements of Haller et al. (2002) of a barred beach with channels. Results fit with previous simulations performed by other models and with available observational data. Finally, a realistic case is simulated with energetic waves travelling over a coast of the Gulf of Lion (in the northwest of the Mediterranean Sea) for which currents are available at different depths as well as an accurate bathymetric database of the 0–10 m depth range. A grid nesting approach is used to account for the different forcings acting at different spatial scales. The simulation coupling the effects of waves and currents is successful to reproduce the powerful northward littoral drift in the 0–15 m depth zone. More precisely, two distinct cases are identified: When waves have a normal angle of incidence with the coast, they are responsible for complex circulation cells and rip currents in the surf zone, and when they travel obliquely, they generate a northward littoral drift. These features are more complicated than in the test cases, due to the complex bathymetry and the consideration of wind and non-stationary processes. Wave impacts in the inner shelf are less visible since wind and regional circulation seem to be the predominant forcings. Besides, a discrepancy between model and observations is noted at that scale, possibly linked to an underestimation of the wind stress. This three-dimensional method allows a good representation of vertical current profiles and permits the calculation of the shear stress associated with waves and currents. Future work will focus on the combination with a sediment transport model.

Thanks to its optimal location on the northern Brazilian margin, core MD09-3257 records both ocean circulation and atmospheric changes. The latter occur locally in the form of increased rainfall on the adjacent continent during the cold intervals recorded in Greenland ice and northern North Atlantic sediment cores (i.e., Greenland stadials). These rainfall events are recorded in MD09-3257 as peaks in ln(Ti ∕ Ca). New sedimentary Pa ∕ Th data indicate that mid-depth western equatorial water mass transport decreased during all of the Greenland stadials of the last 40 kyr. Using cross-wavelet transforms and spectrogram analysis, we assess the relative phase between the MD09-3257 sedimentary Pa ∕ Th and ln(Ti ∕ Ca) signals. We show that decreased water mass transport between a depth of ∼1300 and 2300 m in the western equatorial Atlantic preceded increased rainfall over the adjacent continent by 120 to 400 yr at Dansgaard–Oeschger (D–O) frequencies, and by 280 to 980 yr at Heinrich-like frequencies. We suggest that the large lead of ocean circulation changes with respect to changes in tropical South American precipitation at Heinrich-like frequencies is related to the effect of a positive feedback involving iceberg discharges in the North Atlantic. In contrast, the absence of widespread ice rafted detrital layers in North Atlantic cores during D–O stadials supports the hypothesis that a feedback such as this was not triggered in the case of D–O stadials, with circulation slowdowns and subsequent changes remaining more limited during D–O stadials than Heinrich stadials.

La faune des poissons d’eau douce, saumâtre ou marine, présente une forte diversité d’espèces aux styles de vie multiples. Les poissons évoluent dans des habitats diversifiés, offrant des ressources et des possibilités d’utilisation variées. Une ressource se définit selon les besoins de l’individu vis-à-vis de paramètres abiotiques ou biotiques, et se décline en critères de qualité et de quantité. Les déplacements du poisson au cours de sa vie lui permettent d’ajuster ses besoins aux ressources disponibles. Les choix réalisés tendent vers une optimisation des gains d’énergie et du succès reproducteur de l’individu. Ainsi peut-on voir, chez une même espèce, différentes stratégies d’utilisation des ressources donnant lieu à des déplacements d’ampleur variée selon l’échelle de temps considérée. Notamment, les migrations qui mettent en jeu des allers-retours à des stades ontogéniques différents modifient de manière significative les traits reproducteurs et le fonctionnement des populations. L’existence de variants migratoires est alors un point central de l’évolution de ses populations. Le mémoire s’appuie sur mes travaux en cours ou réalisés dans l’équipe, en mettant l’accent sur l’apport des traceurs naturels (isotopes stables particulièrement) à l’étude des ressources et des déplacements chez les poissons.