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Three-dimensional direct numerical simulations (DNS) of the nonlinear dynamics and a route to chaos in a rotating fluid subjected to lateral heating are presented here and discussed in the context of laboratory experiments in the baroclinic annulus. Following two previous preliminary studies, the fluid used is air rather than a liquid as used in all other previous work. This study investigates a bifurcation sequence from the axisymmetric flow to a number of complex flows. The transition sequence, on increase of the rotation rate, from the axisymmetric solution via a steady fully developed baroclinic wave to chaotic flow, followed a variant of the classical quasi-periodic bifurcation route, starting with a subcritical Hopf and associated saddle-node bifurcation. This was followed by a sequence of two supercritical Hopf-type bifurcations, first to an amplitude vacillation, then to a three-frequency quasi-periodic modulated amplitude vacillation (MAV), and finally to a chaotic (MAV). In the context of the baroclinic annulus this sequence is unusual as the vacillation is usually found on decrease of the rotation rate from the steady wave flow. Further transitions of a steady wave with a higher wavenumber pointed to the possibility that a barotropic instability of the sidewall boundary layers and the subsequent breakdown of these barotropic vortices may play a role in the transition to structural vacillation and, ultimately, geostrophic turbulence.

The elliptical instability can take place in planetary cores and stars elliptically deformed by gravitational effects, where it generates large-scale three-dimensional flows assumed to be dynamo capable. In this work, we present the first magneto-hydrodynamic numerical simulations of such flows, using a finite-element method. We first validate our numerical approach by comparing with kinematic and dynamic dynamos benchmarks of the literature. We then systematically study the magnetic field induced by various modes of the elliptical instability from an imposed external field in a triaxial ellipsoidal geometry, relevant in a geo- and astrophysical context. Finally, in tidal induction cases, the external magnetic field is suddenly shut down and the decay rates of the magnetic field are systematically reported.

The stability of a rotating flow in a triaxial ellipsoidal shell with an imposed temperature difference between inner and outer boundaries is studied numerically. We demonstrate that (i) a stable temperature field encourages the tidal instability, (ii) the tidal instability can grow on a convective flow, which confirms its relevance to geo- and astrophysical contexts and (iii) its growth rate decreases when the intensity of convection increases. Simple scaling laws characterizing the evolution of the heat flux based on a competition between viscous and thermal boundary layers are derived analytically and verified numerically. Our results confirm that thermal and tidal effects have to be simultaneously taken into account when studying geophysical and astrophysical flows.

The full non-linear evolution of the tidal instability is studied numerically in an ellipsoidal fluid domain relevant for planetary cores applications. Our numerical model, based on a finite element method, is first validated by reproducing some known analytical results. This model is then used to address open questions that were up to now inaccessible using theoretical and experimental approaches. Growth rates and mode selection of the instability are systematically studied as a function of the aspect ratio of the ellipsoid and as a function of the inclination of the rotation axis compared to the deformation plane. We also quantify the saturation amplitude of the flow driven by the instability and calculate the viscous dissipation that it causes. This tidal dissipation can be of major importance for some geophysical situations and we thus derive general scaling laws which are applied to typical planetary cores.

The onset of small-scale fluctuations around a steady convection pattern in a rotating baroclinic annulus filled with air is investigated using Direct Numerical Simulation. In previous laboratory experiments of baroclinic waves, such fluctuations have been associated with a flow regime termed Structural Vacillation which is regarded as the first step in the transition to fully-developed geostrophic turbulence.

Three-dimensional Direct Numerical Simulation (DNS) on the nonlinear dynamics and a route to chaos in a rotating fluid subjected to lateral heating is presented here and discussed in the context of laboratory experiments in the baroclinic annulus. Following two previous preliminary studies by Maubert and Randriamampianina, the fluid used is air rather than a liquid as used in all other previous work. This study investigated a bifurcation sequence from the axisymmetric flow to a number of complex flows. The transition sequence, on increase of the rotation rate, from the axisymmetric solution via a steady, fully-developed baroclinic wave to chaotic flow followed a variant of the classical quasi-periodic bifurcation route, starting with a subcritical Hopf and associated saddle-node bifurcation. This was followed by a sequence of two supercritical Hopf-type bifurcations, first to an amplitude vacillation, then to a three-frequency quasi-periodic modulated amplitude vacillation (MAV), and finally to a chaotic MAV\\@. In the context of the baroclinic annulus this sequence is unusual as the vacillation is usually found on decrease of the rotation rate from the steady wave flow. Further transitions of a steady wave with a higher wave number pointed to the possibility that a barotropic instability of the side wall boundary layers and the subsequent breakdown of these barotropic vortices may play a role in the transition to structural vacillation and, ultimately, geostrophic turbulence.

Objective Gut microbiota metabolises bile acids (BA). As dysbiosis has been reported in inflammatory bowel diseases (IBD), we aim to investigate the impact of IBD-associated dysbiosis on BA metabolism and its influence on the epithelial cell inflammation response. Design Faecal and serum BA rates, expressed as a proportion of total BA, were assessed by high-performance liquid chromatography tandem mass spectrometry in colonic IBD patients (42) and healthy subjects (29). The faecal microbiota composition was assessed by quantitative real-time PCR. Using BA profiles and microbiota composition, cluster formation between groups was generated by ranking models. The faecal BA profiles in germ-free and conventional mice were compared. Direct enzymatic activities of BA biotransformation were measured in faeces. The impact of BA on the inflammatory response was investigated in vitro using Caco-2 cells stimulated by IL-1β. Results IBD-associated dysbiosis was characterised by a decrease in the ratio between Faecalibacterium prausntizii and Escherichia coli. Faecal-conjugated BA rates were significantly higher in active IBD, whereas, secondary BA rates were significantly lower. Interestingly, active IBD patients exhibited higher levels of faecal 3-OH-sulphated BA. The deconjugation, transformation and desulphation activities of the microbiota were impaired in IBD patients. In vitro, secondary BA exerted anti-inflammatory effects, but sulphation of secondary BAs abolished their anti-inflammatory properties. Conclusions Impaired microbiota enzymatic activity observed in IBD-associated dysbiosis leads to modifications in the luminal BA pool composition. Altered BA transformation in the gut lumen can erase the anti-inflammatory effects of some BA species on gut epithelial cells and could participate in the chronic inflammation loop of IBD.

N-acyl homoserine lactones (AHLs), which are autoinducer quorum-sensing molecules involved in the bacterial communication network, also interact with eukaryotic cells. Searching for these molecules in the context of inflammatory bowel disease (IBD) is appealing. The aims of our study were to look for AHL molecules in faecal samples from healthy subjects (HS) and IBD patients to correlate AHL profiles with the microbiome and investigate the effect of AHLs of interest on epithelial cells. Using mass spectrometry, we characterised AHL profiles in faecal samples from HS (n = 26) and IBD patients in remission (n = 24) and in flare (n = 25) and correlated the presence of AHLs of interest with gut microbiota composition obtained by real-time qPCR and 16S sequencing. We synthesised AHLs of interest to test the inflammatory response after IL1β stimulation and paracellular permeability on Caco-2 cells. We observed 14 different AHLs, among which one was prominent. This AHL corresponded to 3-oxo-C12:2 and was found significantly less frequently in IBD patients in flare (16%) and in remission (37.5%) versus HS (65.4%) (p = 0.001). The presence of 3-oxo-C12:2 was associated with significantly higher counts of Firmicutes, especially Faecalbacterium prausnitzii, and lower counts of Escherichia coli. In vitro, 3-oxo-C12:2 exerted an anti-inflammatory effect on Caco-2 cells. Interestingly, although 3-oxo-C12, the well-known AHL from Pseudomonas aeruginosa, increased paracellular permeability, 3-oxo-C12:2 did not. We identified AHLs in the human gut microbiota and discovered a new and prominent AHL, 3-oxo-C12:2, which correlates with normobiosis and exerts a protective effect on gut epithelial cells.

The blood–brain barrier (BBB) has been defined as a critically important protective barrier that is involved in providing essential biologic, physiologic, and immunologic separation between the central nervous system (CNS) and the periphery. Insults to the BBB can cause overall barrier damage or deregulation of the careful homeostasis maintained between the periphery and the CNS. These insults can, therefore, yield numerous phenotypes including increased overall permeability, interendothelial gap formation, alterations in cytokine and chemokine secretion, and accelerated cellular passage. The current studies expose the human brain microvascular endothelial cell line, hCMEC/D3, to prolonged morphine exposure and aim to uncover the mechanisms underlying alterations in barrier function in vitro. These studies show alterations in the mRNA and protein levels of the cellular adhesion molecules (CAMs) intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and activated leukocyte cell adhesion molecule that correlate with an increased firm adhesion of the CD3+ subpopulation of peripheral blood mononuclear cells (PBMCs). Overall, these studies suggest that prolonged morphine exposure may result in increased cell migration into the CNS, which may accelerate pathological processes in many diseases that involve the BBB.