Tectonic and metamorphic evolution of the Central Himalayan Domain in Southeast Zanskar (Kashmir, India)

La région du Zanskar, étudiée dans le cadre de ce travail, se situe au passage entre deux domaines himalayens fortement contrastés, la Séquence Cristalline du Haut Himalaya (HHCS), composée de roches métamorphiques et l'Himalaya Tethysien (TH), composé de séries sédimentaires. La transition entre ces deux domaines est marquée par une structure tectonique majeure, la Zone de Cisaillement du Zanskar (ZSZ), au sein de laquelle on observe une augmentation extrêmement rapide, mais néanmoins graduelle, du degré du métamorphisme entre le TH et le HHCS. Il a été établi que le HHCS n'est autre que l'équivalent métamorphique des séries sédimentaires de la base du TH. C'est principalement lors d'un épisode de mise en place de nappes à vergence sudouest, entre l'Eocène moyen et l'Oligocène, que les séries sédimentaires de la base du TH ont été entraînées en profondeur où elles ont subi un métamorphisme de type barrovien. Au début du Miocène, le HHCS à été exhumé en direction du sud-ouest sous forme d'une grande nappe, délimitée a sa base par le MCT (principal chevauchement central) et à son sommet par la Zone de Cisaillement du Zanskar. L'ensemble des zones barroviennes, de la zone à biotite jusqu'à la zone à disthène, a été cisaillée par les mouvements en faille normale au sommet du HHCS et se retrouve actuellement sur une épaisseur d'environ 1 kilomètre au sein de la ZSZ. La décompression associée à l'exhumation du HHCS a provoqué la fusion partielle d'une partie du HHCS et a donné naissance à des magmas de composition leucogranitiques. Grâce à la géothermobarometrie, et connaissant la géométrie de la ZSZ, il nous a été possible de déterminer que le rejet le long de cette structure d'extension est d'au moins 35?9 kilomètres. Une série d'arguments nous permet cependant de suggérer que ce rejet aurait pu être encore bien plus important (~100km). Les données géochronologiques nous permettent de contraindre la durée des mouvements d'extension le long de la ZSZ à 2.4?0.2 Ma entre 22.2?0.2 Ma et 19.8?0.1 Ma. Ce travail apporte de nouvelles données sur les processus métamorphiques, magmatiques et tectoniques liés aux phénomènes d'extension syn-orogeniques.<br/><br/>The southeastern part of Zanskar is located at the transition between two major Himalayan domains of contrasting metamorphic grade, the High Himalayan Crystalline Sequence (HHCS) and the Tethyan Himalaya (TH). The transition between the TH and the HHCS is marked by a very rapid, although perfectly gradual, decrease in metamorphic grade, which coincides with a major tectonic structure, the Zanskar Shear Zone (ZSZ). It is now an established fact that the relation between the HHCS and the TH is not one of basement-cover type, but that the metasedimentary series of the HHCS represent the metamorphic equivalent of the lowermost sedimentary series of the TH. This transformation of sedimentary series into metamorphic rocks, and hence the differentiation between the TH and the HHCS, is the consequence of crustal thickening associated to the formation of large scale southwest vergent nappes within the Tethyan Himalaya sedimentary series. This, Middle Eocene to Oligocene, episode of crustal thickening and associated Barrovian metamorphism is followed, shortly after, by the exhumation of the HHCS as a, large scale, south-west vergent, nappe. Foreword The exhumation of the HHCS nappe is marked by the activation of two contemporaneous structures, the Main Central Thrust at its base and the Zanskar Shear Zone at its top. Extensional movements along the ZSZ, caused the Barrovian biotite to the kyanite zones to be sheared and constricted within the ~1 km thick shear zone. Decompression associated with the exhumation of the HHCS induced the formation of leucogranitic magmas through vapour-absent partial melting of the highest-grade rocks. The combination of geothermobarometric data with a geometric model of the ZSZ allowed us to constrain the net slip at the top of the HHCS to be at least 35?9 kilometres. A set of arguments however suggests that these movements might have been much more important (~ 100 km). Geochronological data coupled with structural observations constrain the duration of ductile shearing along the ZSZ to 2.4?0.2 Ma between 22.2?0.2 Ma and 19.8?0.1 Ma. This study also addresses the consequences of synorogenic extension on the metamorphic, tectonic and magmatic evolution of the upper parts of the High Himalayan Crystalline Sequence.

Evolution based on domain combinations: the case of glutaredoxins

Background: Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX) domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear. Results: In this work we analyze the distribution and evolution of GRX proteins in archaea,bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life. Conclusion: Our results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.

The impact of balancing on problem hardness in a highly structured domain

Random problem distributions have played a key role in the study and design of algorithms for constraint satisfaction and Boolean satisfiability, as well as in ourunderstanding of problem hardness, beyond standard worst-case complexity. We consider random problem distributions from a highly structured problem domain that generalizes the Quasigroup Completion problem (QCP) and Quasigroup with Holes (QWH), a widely used domain that captures the structure underlying a range of real-world applications. Our problem domain is also a generalization of the well-known Sudoku puz- zle: we consider Sudoku instances of arbitrary order, with the additional generalization that the block regions can have rectangular shape, in addition to the standard square shape. We evaluate the computational hardness of Generalized Sudoku instances, for different parameter settings. Our experimental hardness results show that we can generate instances that are considerably harder than QCP/QWH instances of the same size. More interestingly, we show the impact of different balancing strategies on problem hardness. We also provide insights into backbone variables in Generalized Sudoku instances and how they correlate to problem hardness.

Multilayer switch hardware support for Linux

VDSL on teknologia, joka mahdollistaa nopeat Internet-yhteydet tavallista puhelinlinjaa käyttäen. Tätä varten käyttäjä tarvitsee VDSL-modeemin ja Internet-operaattori reitittimen, johon VDSL-linjat kytketään. Reitittimen on oltava suorituskykyinen, jotta kaikki VDSL-liikenne voidaan reittittää eteenpäin. Tehokkuutta haetaan tekemällä suuri osa reitityksestä erityisillä reititinpiireillä. Tässä diplomityössä käsitellään reititinpiirien teoriaa ja niiden hallintaa. Lisäksi vertailtiin kolmen suuren valmistajan tuotteita. Tuotteiden tarjoamat ominaisuudet vaikuttivat hyvin yhteneväisiltä. Ominaisuuksien hallinta ja toteutus olivat erilaisia. Työn tavoitteena oli löytää ohjelmistoarkkitehtuuri piirien ohjaamiseen niin, että Linux-käyttöjärjestelmän ytimen palveluja voitaisiin käyttää mahdollisimman hyödyllisesti. Työssä havaittiin, että ohjelmistoarkkitehtuurin voi määritellä monella eri tavalla riippuen siitä, miten piiri on kytketty prosessoriin, mitä piirin ominaisuuksia halutaan käyttää ja miten arkkitehtuuria halutaan jatkossa laajentaa.

Langevin equations with multiplicative noise: Application to domain growth

Langevin Equations of Ginzburg-Landau form, with multiplicative noise, are proposed to study the effects of fluctuations in domain growth. These equations are derived from a coarse-grained methodology. The Cahn-Hiliard-Cook linear stability analysis predicts some effects in the transitory regime. We also derive numerical algorithms for the computer simulation of these equations. The numerical results corroborate the analytical predictions of the linear analysis. We also present simulation results for spinodal decomposition at large times.

IPSec in 3G packet switched domain

Diplomityö käsittelee IPSec-protokollan (IP Security Protocol) implementointia UMTS:n (Universal Mobile Telecommunications System) pakettikytkentäiseen verkkoon. Runkoverkkoa käytetään mobiilikäyttäjän datan siirtämiseen sekä verkkoelementtien väliseen ohjausinformaation välitykseen. Koska UMTS:n runkoverkot ovat IP-pakettikytkentäisiä verkkoja, IPSec-protokollaa voidaan käyttää lähetettyjen IP-datasähkeiden suojaamiseen. IPSec- ja IKE-protokollien (Internet Key Exchange) käyttö on koettu monimutkaiseksi kiinteissä verkoissa. Tämän saman ongelman edessä tulevat olemaan myös operaattorit, kun he alkavat rakentaa UMTS-verkkojaan. On kuitenkin muistettava se, että tulevaisuudessa lähes kaikki data mukaanlukien ääni ja video on tarkoitus siirtää IP-protokollan avulla. IP-teknologiaan perustuva tiedonsiirron kasvu lisää IPSec-protokollan merkitystä ei ainoastaan runkoverkossa mutta myös radioliityntäverkoissa sekä SS7-merkinantoverkoissa (Signaling System No. 7). Diplomityö on tehty osaksi diplomi-insinöörin tutkintoa Lappeenrannan teknillisessä yliopistossa. Työ on tehty Nokia Networksin palveluksessa Helsingissä, vuosien 2002 ja 2003 välisenä aikana.

Differential Dimerization of Variants Linked to Enhanced S-Cone Sensitivity Syndrome (ESCS) Located in the NR2E3 Ligand-Binding Domain.

NR2E3 encodes the photoreceptor-specific nuclear hormone receptor that acts as a repressor of cone-specific gene expression in rod photoreceptors, and as an activator of several rod-specific genes. Recessive variants located in the ligand-binding domain (LBD) of NR2E3 cause enhanced short wavelength sensitive- (S-) cone syndrome (ESCS), a retinal degeneration characterized by an excess of S-cones and non-functional rods. We analyzed the dimerization properties of NR2E3 and the effect of disease-causing LBD missense variants by bioluminescence resonance energy transfer (BRET(2) ) protein interaction assays. Homodimerization was not affected in presence of p.A256V, p.R039G, p.R311Q, and p.R334G variants, but abolished in presence of p.L263P, p.L336P, p.L353V, p.R385P, and p.M407K variants. Homology modeling predicted structural changes induced by NR2E3 LBD variants. NR2E3 LBD variants did not affect interaction with CRX, but with NRL and rev-erbα/NR1D1. CRX and NRL heterodimerized more efficiently together, than did either with NR2E3. NR2E3 did not heterodimerize with TLX/NR2E1 and RXRα/NR2C1. The identification of a new compound heterozygous patient with detectable rod function, who expressed solely the p.A256V variant protein, suggests a correlation between LBD variants able to form functional NR2E3 dimers and atypical mild forms of ESCS with residual rod function.

Ras-association domain of sorting nexin 27 is critical for regulating expression of GIRK potassium channels

G protein-gated inwardly rectifying potassium (GIRK) channels play an important role in regulating neuronal excitability. Sorting nexin 27b (SNX27b), which reduces surface expression of GIRK channels through a PDZ domain interaction, contains a putative Ras-association (RA) domain with unknown function. Deleting the RA domain in SNX27b (SNX27b-DRA) prevents the down-regulation of GIRK2c/GIRK3 channels. Similarly, a point mutation (K305A) in the RA domain disrupts regulation of GIRK2c/GIRK3 channels and reduces H-Ras binding in vitro. Finally, the dominant-negative H-Ras (S17N) occludes the SNX27b-dependent decrease in surface expression of GIRK2c/GIRK3 channels. Thus, the presence of a functional RA domain and the interaction with Ras-like G proteins comprise a novel mechanism for modulating SNX27b control of GIRK channel surface expression and cellular excitability.

RasGAP Shields Akt from Deactivating Phosphatases in Fibroblast Growth Factor Signaling but Loses This Ability Once Cleaved by Caspase-3.

Fibroblast growth factor receptors (FGFRs) are involved in proliferative and differentiation physiological responses. Deregulation of FGFR-mediated signaling involving the Ras/PI3K/Akt and the Ras/Raf/ERK MAPK pathways is causally involved in the development of several cancers. The caspase-3/p120 RasGAP module is a stress sensor switch. Under mild stress conditions, RasGAP is cleaved by caspase-3 at position 455. The resulting N-terminal fragment, called fragment N, stimulates anti-death signaling. When caspase-3 activity further increases, fragment N is cleaved at position 157. This generates a fragment, called N2, that no longer protects cells. Here, we investigated in Xenopus oocytes the impact of RasGAP and its fragments on FGF1-mediated signaling during G2/M cell cycle transition. RasGAP used its N-terminal Src homology 2 domain to bind FGFR once stimulated by FGF1, and this was necessary for the recruitment of Akt to the FGFR complex. Fragment N, which did not associate with the FGFR complex, favored FGF1-induced ERK stimulation, leading to accelerated G2/M transition. In contrast, fragment N2 bound the FGFR, and this inhibited mTORC2-dependent Akt Ser-473 phosphorylation and ERK2 phosphorylation but not phosphorylation of Akt on Thr-308. This also blocked cell cycle progression. Inhibition of Akt Ser-473 phosphorylation and entry into G2/M was relieved by PHLPP phosphatase inhibition. Hence, full-length RasGAP favors Akt activity by shielding it from deactivating phosphatases. This shielding was abrogated by fragment N2. These results highlight the role played by RasGAP in FGFR signaling and how graded stress intensities, by generating different RasGAP fragments, can positively or negatively impact this signaling.

Computational toolbox towards evolutionary domain mapping of membrane proteins

Membrane proteins account for about 20% to 30% of all proteins encoded in a typical genome. They play central roles in multiple cellular processes mediating the interaction of the cell with its surrounding. Over 60% of all drug targets contain a membrane domain. The experimental difficulties of obtaining a crystal structural severely limits our ability or understanding of membrane protein function. Computational evolutionary studies of proteins are crucial for the prediction of 3D structures. In this project, we construct a tool able to quantify the evolutionary positive selective pressure on each residue of membrane proteins through maximum likelihood phylogeny reconstruction. The conservation plot combined with a structural homology model is also a potent tool to predict those residues that have essentials roles in the structure and function of a membrane protein and can be very useful in the design of validation experiments.

Allosteric conversation in the androgen receptor ligand-binding domain surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. We previously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design.

Domain matched epitaxial growth of Bi1.5Zn1Nb1.5O7 thin films by pulsed laser deposition

Bi1.5Zn1Nb1.5O7 (BZN) epitaxial thin films were grown by pulsed laser deposition on Al2O3 with a double ZnO buffer layer through domain matching epitaxy (DME) mechanism. The pole figure analysis and reciprocal space mapping revealed the single crystalline nature of the thin film. The pole figure analysis also shows a 60º twinning for the (222) oriented crystals. Sharp intense spots in the SAED pattern also indicate the high crystalline nature of BZN thin film. The Fourier filtered HRTEM images of the BZN-ZnO interface confirms the domain matched epitaxy of BZN with ZnO buffer. An electric field dependent dielectric tunability of 68% was obtained for the BZN thin films with inter digital capacitors patterned over the film.

Switch to etravirine for HIV-positive patients receiving statin treatment: a prospective study.

BACKGROUND: Lifestyle changes and statins are the cornerstones in management of dyslipidaemia in patients with HIV infection. Replacement of an antiretroviral therapy (ART) component is a proposed therapeutic strategy to reduce cardiovascular risk. In dyslipidaemic patients with HIV infection, we assessed the efficacy of replacing boosted protease inhibitor (bPI) or efavirenz (EFV) by etravirine (ETR) as an alternative to statin therapy. MATERIALS AND METHODS: A prospective, open-label, multicentre, 12-week study of patients with HIV infection on ART including bPI or EFV, and statin treatment. Four weeks after statin interruption, bPI or EFV was switched to ETR (400 mg, 8 weeks) if serum low-density lipoprotein cholesterol (LDL-C) was ≥ 3 mM. The primary endpoint was the proportion of patients on ETR with no indication for statin treatment at study completion. Serum levels of HIV RNA, lipids and biomarkers of cardiovascular disease were also measured. (ClinicalTrials.gov: NCT01543035). RESULTS: The 31 included patients had a HIV-1 RNA < 50 copies/mL (median age, 52 years; median CD4, 709 cell/mL; median LDL-C, 2·89 mM), 68% were on EFV, and 32% were on bPI. At week 4, 27 patients switched to ETR. At study completion, 15 patients (56%) on ETR did not qualify for statin treatment. After the ETR switch, serum levels of the cardiovascular biomarkers sICAM and MCP1/CCL2 decreased by 11·2% and 18·9%, respectively, and those of CCL5/RANTES and tissue inhibitor of metalloproteinase-1 increased by 14·3% and 13·4%, respectively, indicating reduced cardiovascular risk. There were no notable treatment-related adverse events. CONCLUSIONS: Replacing bPI or EFV by ETR is a viable strategy to obviate primary prevention statin treatment.

Jagged1 intracellular domain-mediated inhibition of Notch1 signalling regulates cardiac homeostasis in the postnatal heart.

AIMS: Notch1 signalling in the heart is mainly activated via expression of Jagged1 on the surface of cardiomyocytes. Notch controls cardiomyocyte proliferation and differentiation in the developing heart and regulates cardiac remodelling in the stressed adult heart. Besides canonical Notch receptor activation in signal-receiving cells, Notch ligands can also activate Notch receptor-independent responses in signal-sending cells via release of their intracellular domain. We evaluated therefore the importance of Jagged1 (J1) intracellular domain (ICD)-mediated pathways in the postnatal heart. METHODS AND RESULTS: In cardiomyocytes, Jagged1 releases J1ICD, which then translocates into the nucleus and down-regulates Notch transcriptional activity. To study the importance of J1ICD in cardiac homeostasis, we generated transgenic mice expressing a tamoxifen-inducible form of J1ICD, specifically in cardiomyocytes. Using this model, we demonstrate that J1ICD-mediated Notch inhibition diminishes proliferation in the neonatal cardiomyocyte population and promotes maturation. In the neonatal heart, a response via Wnt and Akt pathway activation is elicited as an attempt to compensate for the deficit in cardiomyocyte number resulting from J1ICD activation. In the stressed adult heart, J1ICD activation results in a dramatic reduction of the number of Notch signalling cardiomyocytes, blunts the hypertrophic response, and reduces the number of apoptotic cardiomyocytes. Consistently, this occurs concomitantly with a significant down-regulation of the phosphorylation of the Akt effectors ribosomal S6 protein (S6) and eukaryotic initiation factor 4E binding protein1 (4EBP1) controlling protein synthesis. CONCLUSIONS: Altogether, these data demonstrate the importance of J1ICD in the modulation of physiological and pathological hypertrophy, and reveal the existence of a novel pathway regulating cardiac homeostasis.