Studying an Agulhas ring's long-term pathway and decay with finite-time coherent sets

© 2015 AIP Publishing LLC. Coherent sets in dynamical systems are regions in phase space that optimally >carry mass> with them under the system's evolution, so that these regions experience minimal leakage. The dominant tool for determining coherent sets is the transfer operator, which provides a complete description of Lagrangian mass transport. In this work, we combine existing transfer operator methods with a windowing scheme to study the spatial and temporal evolution of a so-called Agulhas ring: a large anticyclonic mesoscale eddy playing a key role in inter-ocean exchange of climate-relevant properties. Our focus is on ring decay over time and the windowing scheme enables us to study how the most coherent region (our estimate of the ring) varies in position and size over a period of more than two years. We compare the eddy-like structure and its spatio-temporal changes as revealed by our method and by a classical Eulerian approach.The altimeter products were produced by Ssalto/Duacs and distributed by Aviso, with support from CNES (http://www.aviso.oceanobs.com/duacs/). G.F. and C.H. were partially supported by the 2011/12 Go8/DAAD Australia/Germany Joint Research Co-Operation Scheme. G.F. was also supported by an ARC Future Fellowship. E.v.S. was supported by the ARC via Grant DE130101336. V.R. acknowledges support from MICINN and FEDER through the ESCOLA project (CTM2012-39025-C02-01) while finishing this paper.Peer Reviewe

Seasonal variability of the subpolar gyres in the Southern Ocean: a numerical investigation based on transfer operators

The detection of regions in the ocean that are coherent over an extended period of time is a fundamental problem in many oceanic applications. For instance such regions are important for studying the transport of marine species and for the distribution of nutrients. In this study we demonstrate the efficacy of transfer operators in detecting and analysing such structures. We focus first on the detection of the Weddell and Ross Gyre for the four seasons spanning December 2003–November 2004 within the 3-D oceanic domain south of 30° S, and show distinct seasonal differences in both the three-dimensional structure and the persistence of the gyres. Further, we demonstrate a new technique based on the discretised transfer operators to calculate the mean residence time of water within parts of the gyres and determine pathways of water leaving and entering the gyres

HIV-1 Nef Induces Proinflammatory State in Macrophages through Its Acidic Cluster Domain: Involvement of TNF Alpha Receptor Associated Factor 2

Background: HIV-1 Nef is a virulence factor that plays multiple roles during HIV replication. Recently, it has been described that Nef intersects the CD40 signalling in macrophages, leading to modification in the pattern of secreted factors that appear able to recruit, activate and render T lymphocytes susceptible to HIV infection. The engagement of CD40 by CD40L induces the activation of different signalling cascades that require the recruitment of specific tumor necrosis factor receptor-associated factors (i.e. TRAFs). We hypothesized that TRAFs might be involved in the rapid activation of NF-kappa B, MAPKs and IRF-3 that were previously described in Nef-treated macrophages to induce the synthesis and secretion of proinflammatory cytokines, chemokines and IFN beta to activate STAT1, -2 and -3. Methodology/Principal Findings: Searching for possible TRAF binding sites on Nef, we found a TRAF2 consensus binding site in the AQEEEE sequence encompassing the conserved four-glutamate acidic cluster. Here we show that all the signalling effects we observed in Nef treated macrophages depend on the integrity of the acidic cluster. In addition, Nef was able to interact in vitro with TRAF2, but not TRAF6, and this interaction involved the acidic cluster. Finally silencing experiments in THP-1 monocytic cells indicate that both TRAF2 and, surprisingly, TRAF6 are required for the Nef-induced tyrosine phosphorylation of STAT1 and STAT2. Conclusions: Results reported here revealed TRAF2 as a new possible cellular interactor of Nef and highlighted that in monocytes/macrophages this viral protein is able to manipulate both the TRAF/NF-kappa B and TRAF/IRF-3 signalling axes, thereby inducing the synthesis of proinflammatory cytokines and chemokines as well as IFN beta

Structural insight into the membrane targeting domain of the Legionella deAMPylase SidD

AMPylation, the post-translational modification with adenosine monophosphate (AMP), is catalyzed by effector proteins from a variety of pathogens. Legionella pneumophila is thus far the only known pathogen that, in addition to encoding an AMPylase (SidM/DrrA), also encodes a deAMPylase, called SidD, that reverses SidM-mediated AMPylation of the vesicle transport GTPase Rab1. DeAMPylation is catalyzed by the N-terminal phosphatase-like domain of SidD. Here, we determined the crystal structure of full length SidD including the uncharacterized C-terminal domain (CTD). A flexible loop rich in aromatic residues within the CTD was required to target SidD to model membranes in vitro and to the Golgi apparatus within mammalian cells. Deletion of the loop (??loop) or substitution of its aromatic phenylalanine residues rendered SidD cytosolic, showing that the hydrophobic loop is the primary membrane-targeting determinant of SidD. Notably, deletion of the two terminal alpha helices resulted in a CTD variant incapable of discriminating between membranes of different composition. Moreover, a L. pneumophila strain producing SidD??loop phenocopied a L. pneumophila ??sidD strain during growth in mouse macrophages and displayed prolonged co-localization of AMPylated Rab1 with LCVs, thus revealing that membrane targeting of SidD via its CTD is a critical prerequisite for its ability to catalyze Rab1 deAMPylation during L. pneumophila infection

Three-dimensional characterization and tracking of an Agulhas Ring

A novel probabilistic methodology is applied to identify optimally coherent structures associated with Agulhas Rings, within a time varying velocity field in the South Atlantic Ocean, as simulated by an eddy-permitting ocean general model. It is shown that this technique provides a way of identifying the three-dimensional shape of a particular Ring in the upper ocean and tracking its evolution over space and time. Based on this three-dimensional representation we can accurately measure the amount of water mass remaining in an Agulhas Ring over time and consequently how much heat or salt is released from the structure as it decays. Identification techniques based on relative vorticity or the Okubo-Weiss parameter have previously been developed for a surface snapshot. Extending these methods in the vertical direction in the upper ocean and comparing the decay of all three-dimensional structures obtained by different methods, we demonstrate that our technique is able to define structures that are more coherent over time than classical methods. While our investigation concentrates on a single Agulhas Ring located in the Cape-Basin from May 2000 over 6. months, the technique may be extended to examine multiple Rings and other coherent structures that are involved in the Agulhas leakage. © 2012 Elsevier Ltd

Three-dimensional characterization and tracking of an Agulhas Ring

A novel probabilistic methodology is applied to identify optimally coherent structures associated with Agulhas Rings, within a time varying velocity field in the South Atlantic Ocean, as simulated by an eddy-permitting ocean general model. It is shown that this technique provides a way of identifying the three-dimensional shape of a particular Ring in the upper ocean and tracking its evolution over space and time. Based on this three-dimensional representation we can accurately measure the amount of water mass remaining in an Agulhas Ring over time and consequently how much heat or salt is released from the structure as it decays. Identification techniques based on relative vorticity or the Okubo-Weiss parameter have previously been developed for a surface snapshot. Extending these methods in the vertical direction in the upper ocean and comparing the decay of all three-dimensional structures obtained by different methods, we demonstrate that our technique is able to define structures that are more coherent over time than classical methods. While our investigation concentrates on a single Agulhas Ring located in the Cape-Basin from May 2000 over 6. months, the technique may be extended to examine multiple Rings and other coherent structures that are involved in the Agulhas leakage. © 2012 Elsevier Ltd