Adaptive Mechanisms of an Estuarine Synechococcus based on Genomics, Transcriptomics, and Proteomics

Picocyanobacteria are important phytoplankton and primary producers in the ocean. Although extensive work has been conducted for picocyanobacteria (i.e. Synechococcus and Prochlorococcus) in coastal and oceanic waters, little is known about those found in estuaries like the Chesapeake Bay. Synechococcus CB0101, an estuarine isolate, is more tolerant to shifts in temperature, salinity, and metal toxicity than coastal and oceanic Synechococcus strains, WH7803 and WH7805. Further, CB0101 has a greater sensitivity to high light intensity, likely due to its adaptation to low light environments. A complete and annotated genome sequence of CB0101 was completed to explore its genetic capacity and to serve as a basis for further molecular analysis. Comparative genomics between CB0101, WH7803, and WH7805 show that CB0101 contains more genes involved in regulation, sensing, and stress response. At the transcript and protein level, CB0101 regulates its metabolic pathways, transport systems, and sensing mechanisms when nitrate and phosphate are limited. Zinc toxicity led to oxidative stress and a global down regulation of photosystems and the translation machinery. From the stress response studies seven chromosomal toxin-antitoxin (TA) genes, were identified in CB0101, which led to the discovery of TA genes in several marine Synechococcus strains. The activation of the relB2/relE1 TA system allows CB0101 to arrest its growth under stressful conditions, but the growth arrest is reversible, once the stressful environment dissipates. The genome of CB0101 contains a relatively large number of genomic island (GI) genes compared to known marine Synechococcus genomes. Interestingly, a massive shutdown (255 out of 343) of GI genes occurred after CB0101 was infected by a lytic phage. On the other hand, phage-encoded host-like proteins (hli, psbA, ThyX) were highly expressed upon phage infection. This research provides new evidence that estuarine Synechococcus like CB0101 have inherited unique genetic machinery, which allows them to be versatile in the estuarine environment

High resolution 3D laser scanner measurements of a strike-slip fault quantify its morphological anisotropy at all scales

The surface roughness of a recently exhumed strikeslip fault plane has been measured by three independent 3D portable laser scanners. Digital elevation models of several fault surface areas, from 1 m2 to 600 m2, have been measured at a resolution ranging from 5 mm to 80 mm. Out of plane height fluctuations are described by non-Gaussian distribution with exponential long range tails. Statistical scaling analyses show that the striated fault surface exhibits self-affine scaling invariance with a small but significant directional morphological anisotropy that can be described by two scaling roughness exponents, H1 = 0.7 in the direction of slip and H2 = 0.8 perpendicular to the direction of slip

Sea ice inertial oscillations in the Arctic Basin

International audienceAn original method to quantify the amplitude of inertial motion of oceanic and ice drifters, through the introduction of a non-dimensional parameter M defined from a spectral analysis, is presented. A strong seasonal dependence of the magnitude of sea ice inertial oscillations is revealed, in agreement with the corresponding annual cycles of sea ice extent, concentration, thickness, advection velocity, and deformation rates. The spatial pattern of the magnitude of the sea ice inertial oscillations over the Arctic Basin is also in agreement with the sea ice thickness and concentration patterns. This argues for a strong interaction between the magnitude of inertial motion on one hand, the dissipation of energy through mechanical processes, and the cohesiveness of the cover on the other hand. Finally, a significant multi-annual evolution towards greater magnitudes of inertial oscillations in recent years, in both summer and winter, is reported, thus concomitant with reduced sea ice thickness, concentration and spatial extent

Observations d'interactions sismiques et d'une phase de nucléation de grands séismes

Dans cette thèse, nous présentons trois études concernant les interactions entre séismes et la phase de nucléation des forts tremblements de terre. La première partie de ce travail concerne le NO de la Turquie, où deux systèmes tectoniques sont présents : décrochement sur la Faille Nord Anatolienne et extension dans des essaims situés autour de la faille. Nous montrons que ces deux systèmes interagissent, mais répondent différemment à l'excitation du séisme d'Izmit (1999). Les calculs des changements de contraintes de Coulomb induits par le séisme d'Izmit indiquent que les évènements en décrochement répondent aux contraintes dynamiques, alors que les séismes en extension semblent contrôlés par la déformation statique de la croûte. Dans la seconde partie de cette thèse, nous analysons une importante séquence sismique qui s'est produite en 2008 en Grèce. Cette analyse a montré que les séismes en subduction ou en décrochement composant la séquence reflètent le mouvement du SO rigide de la Grèce vers le SSO accompagné du plongement de la plaque Africaine et du retrait vers le sud de la subduction. Cette première étape de déformation est suivie, quelques mois plus tard, de la déformation interne de la plaque Egée qui se manifeste par de l'extension N-S. Cette séquence sismique est le témoin de l'existence d'un couplage dynamique entre la subduction et le prolongement de la Faille Nord Anatolienne dans la région égéenne. Enfin, le but de la dernière partie de cette thèse a été d'apporter des éléments de réponse à la question : existe-t-il un phénomène observable par le biais de la sismicité qui précède de manière systématique les grands tremblements de terre? Pour cela nous avons étudié l'activité sismique précédant des séismes de M$geq 6.5$ dans des régions bien instrumentées (Japon, Cascades et NO des Etats-Unis). Nous montrons que la grande majorité des séismes interplaques est précédée d'une accélération de la sismicité, au contraire des séismes intraplaques. Nous mettons également en évidence une différence entre les séismes en décrochement et les séismes en subduction : les pré-chocs des séismes en subduction sont localisés dans une grande région, rendant un déclenchement en cascade des évènements et du choc principal impossible.We present three studies about earthquake interactions and the nucleation phase of big earthquakes. The first part of this work deals with the northwestern Turkey, where two tectonic regimes exist, with the transform North Anatolian Fault and extension clusters around it. We show that these two systems interact, but respond differently to Izmit earthquake (1999) stimulation. Computations of the Coulomb stress changes induced by the Izmit earthquake indicate that strike-slip events respond to dynamic stresses, whereas the extension ones seem to be controlled by the static deformation of the crust. In the second part, we analyze a seismic sequence that occurred in 2008 in Greece. This analysis shows that subduction or strike-slip earthquakes of the sequence depict the overall motion of the southwestern Greece to the SSW, accompanied by the plunge and the southward retreat of the slab. This first deformation stage is followed, few months later, by the internal deformation of the Aegean plate, which occurs as N-S extension. This seismic sequence depicts the existence of dynamic coupling between the Hellenic subduction and the prolongation of the North Anatolian Fault. The aim of the last part was to shed some lights on the question: is there a systematic seismic phenomena preceding the occurrence of big earthquakes? To do that, we studied seismic activity preceding M$geq$6.5 earthquakes in some well-instrumented areas of the North Pacific. We show that most of the interplate earthquakes are preceded by an increase of the activity, unlike the intraplate ones. We also highlight a different behavior between strike-slip and subduction events: foreshocks of subduction earthquakes are located in a large area, preventing a cascade triggering.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

Slow slip detection with deep learning in multi-station raw geodetic time series validated against tremors in Cascadia

Slow slip events (SSEs) originate from a slow slippage on faults that lasts from a few days to years. A systematic and complete mapping of SSEs is key to characterizing the slip spectrum and understanding its link with coeval seismological signals. Yet, SSE catalogues are sparse and usually remain limited to the largest events, because the deformation transients are often concealed in the noise of the geodetic data. Here we present the first multi-station deep learning SSE detector applied blindly to multiple raw geodetic time series. Its power lies in an ultra-realistic synthetic training set, and in the combination of convolutional and attention-based neural networks. Applied to real data in Cascadia over the period 2007-2022, it detects 78 SSEs, that compare well to existing independent benchmarks: 87.5% of previously catalogued SSEs are retrieved, each detection falling within a peak of tremor activity. Our method also provides useful proxies on the SSE duration and may help illuminate relationships between tremor chatter and the nucleation of the slow rupture. We find an average day-long time lag between the slow deformation and the tremor chatter both at a global- and local-temporal scale, suggesting that slow slip may drive the rupture of nearby small asperities

Effect of the deposition route on the microstructure of plasma-sprayed hydroxyapatite coatings

Plasma-spray (PS) is the most common technique used to cover orthopaedic titanium-based implant surfaces with hydroxyapatite (HA - Ca10(PO4)6OH2). The objective of the current work was to explore the influence of the precursor nature and characteristics (mainly powder size, Ca/P ratio, and density) on the morphology and the microstructure of HA coatings, deposited either by conventional atmospheric plasma spray (APS) or by rf-suspension plasma spray (rf-SPS). Two powders with different size distribution, density and shape were sprayed with same operating APS conditions. In parallel two water-based suspensions with distinct particle size and chemistry (Ca/P ratio) were implemented in rf-SPS. The morphology of both APS and rf-SPS coatings observed by SEM exhibits micro and sub-micro sized structures respectively, with similar porosity and thickness. The difference in precursor particle size does not affect the coating structure in rf-SPS, unlike in APS conditions. Superimposition of topography and phases maps performed from profilometry and Raman cartographies showed no direct correlation between the surface profile and composition. But such analysis highlighted the heterogeneity of the phases composing the coating surface, opening the possibility of a better understanding of biological behaviour

Complete IRAC mapping of the CFHTLS-DEEP, MUSYC AND NMBS-II FIELDS

The IRAC mapping of the NMBS-II fields program is an imaging survey at 3.6 and 4.5$\mu$m with the Spitzer Infrared Array Camera (IRAC). The observations cover three Canada-France-Hawaii Telescope Legacy Survey Deep (CFHTLS-D) fields, including one also imaged by AEGIS, and two MUSYC fields. These are then combined with archival data from all previous programs into deep mosaics. The resulting imaging covers a combined area of about 3 $deg^2$, with at least $\sim$2 hr integration time for each field. In this work, we present our data reduction techniques and document the resulting coverage maps at 3.6 and 4.5$\mu$m. All of the images are W-registered to the reference image, which is either the z-band stack image of the 25\% best seeing images from the CFHTLS-D for CFHTLS-D1, CFHTLS-D3, and CFHTLS-D4, or the K-band images obtained at the Blanco 4-m telescope at CTIO for MUSYC1030 and MUSYC1255. We make all images and coverage maps described herein publicly available via the Spitzer Science Center.Comment: Accepted in PASP; released IRAC mosaics available upon publication of the pape

Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a rol

QuantUM: Quantitative Safety Analysis of UML Models

When developing a safety-critical system it is essential to obtain an assessment of different design alternatives. In particular, an early safety assessment of the architectural design of a system is desirable. In spite of the plethora of available formal quantitative analysis methods it is still difficult for software and system architects to integrate these techniques into their every day work. This is mainly due to the lack of methods that can be directly applied to architecture level models, for instance given as UML diagrams. Also, it is necessary that the description methods used do not require a profound knowledge of formal methods. Our approach bridges this gap and improves the integration of quantitative safety analysis methods into the development process. All inputs of the analysis are specified at the level of a UML model. This model is then automatically translated into the analysis model, and the results of the analysis are consequently represented on the level of the UML model. Thus the analysis model and the formal methods used during the analysis are hidden from the user. We illustrate the usefulness of our approach using an industrial strength case study.Comment: In Proceedings QAPL 2011, arXiv:1107.074