A case of acute retinal pigment epithelitis: spectral domain optical coherence tomography time course and physiopathologic hypothesis.

PURPOSE: To report the time course of retinal morphologic changes in a patient with acute retinal pigment epithelitis (ARPE) using spectral domain optical coherence tomography (SD-OCT). METHODS: A 30-year old man was referred for blurred vision of his right eye after five days that appeared suddenly 15 days after recovery from a flu-like syndrome. SD-OCT was performed immediately, followed by fluorescein and infracyanine angiography at eight days and then at three weeks. RESULTS: At presentation, a bubble of sub-macular deposit was observed on the right macula with central golden micronodules in a honeycomb pattern. SD-OCT showed an "anterior dislocation" of all the retinal layers up to the inner/outer segment (IS/OS) line and irregular deposits at the OS level together with thickening of the retinal pigment epithelial (RPE) layer. As visual acuity increased, eight days later, the OCT showed reduction of the sub-retinal deposits and an abnormal hyperflectivity of the sub-retinal and RPE layers was observed. The patient showed a positive serology for picornavirus. DISCUSSION: The acute SD-OCT sections of this patient with ARPE were compared with histological sections of a 35 day old Royal College of Surgeons rat. Similar findings could be observed, with preservation of the IS/OS line and accumulation of debris at the OS level, suggesting that ARPE symptoms could result from a transient phagocytic dysfunction of the RPE at the fovea, inducing reversible accumulation of undigested OS. Picornaviruses comprising enterovirus and coxsachievirus described as being associated with acute chorioretinitis. In this case, it was responsible for ARPE. CONCLUSION: We hypothesize that ARPE syndrome results from a transient dysfunction of RPE, which can occur as a post viral reaction.

Root distribution of irrigated grapevine rootstocks in a coarse texture soil of the São Francisco Valley, Brazil

An experiment was carried out to determine the root distribution of four grapevine rootstocks (Salt Creek, Dogridge, Courdec 1613, IAC 572) in a coarse texture soil of a commercial growing area in Petrolina County, São Francisco Valley, Brazil. Rootstocks were grafted to a seedless table grape cv. Festival, and irrigated by microsprinkler. Roots were quantified by the trench wall method aided by digital image analysis. Results indicated that roots reached 1 m depth, but few differences among rootstocks were found. All of them presented at least 90 % of the roots distributed until 0.6 m depth, with a greater root presence in the first 0.4 m. The upper 0.6 m can be taken into account as the effective rooting depth for soil and water management.

The Paleozoic magmatic history of the Maggia and Sambuco nappes, Lower Penninic, Central Lepontine Alps

Résumé : Les corps magmatiques sont des indicateurs essentiels dans toute reconstitution paléogéographique et/ou géodynamique d'un cycle orogénique, en particulier en contexte polycyclique, où la plupart des autres indices ont été oblitérés. Ils sont aisément datables et leurs caractéristiques géochimiques permettent de contraindre leur contexte tectonique de mise en place. Cette approche a été appliquée aux socles pré-mésozoïques des nappes penniques inférieures de Sambuco et de la Maggia, dans les Alpes centrales lepontines. Plusieurs événements magmatiques ont été identifiés dans le socle de Sambuco et datés par la méthode U-Pb sur zircon couplée à la technique LA-ICPMS. La suite calco-alcaline mafique rubanée de Scheggia est datée du Cambrien inférieur à 540-530 Ma ; le métagranite alumineux oeillé de Sasso Nero a un âge de 480-470 Ma, tout comme bien d'autres «older orthogneisses» des socles alpins. Il contient des zircons hérités d'âge panafricain à 630-610 Ma, indicateur d'une affiliation gondwanienne de ces terrains. Le pluton calco-alcalin du Matorello est daté à environ 300-310 Ma, et les filons lamprophyriques qu'il abrite à 300 Ma. La granodiorite de Cocco et le leucogranite de Ruscada, tous deux intrudés dans le socle de la nappe adjacente de la Maggia, ont des âges similaires à celui du Matorello. Ceci ajouté aux similitudes magmatiques observées entre Cocco et Matorello suggère une proximité paléogéographique des deux nappes au Permien-Carbonifère. Or ces dernières sont actuellement considérées appartenir à deux domaines paléogéographiques mésozoïques distincts : helvétique pour Sambuco et briançonnais pour Maggia, séparés par un bassin océanique. Si tel fut le cas, aucun mouvement décrochant ne doit avoir décalé les marges continentales de l'océan, retrouvées en parfaite coïncidence lors de sa fermeture. Le Matorello est un pluton recristallisé en faciès amphibolite et plissé par cinq phases successives de déformation non-coaxiales, qui ont conduit à son renversement complet, attesté par des indicateurs de paléogravité. Il préserve de spectaculaires phénomènes de coexistence liquide de magmas (essaims d'enclaves et Bills composites). Ce pluton était originellement tabulaire, construit par l'accumulation de multiples injections de magma en feuillets d'épaisseur métrique à décamétrique. Suivant le rythme de mise en place, les injections successives ont rapidement cristallisé avec des contours nets et bien définis (Bills composites) ou se sont mélangées avec les précédentes pour former une couche non consolidée de plusieurs dizaines de mètres d'épaisseur (granodiorite principale). Les injections individuelles sont délimitées par de subtils contrastes en granulométrie, proportions modales ou ségrégation de minéraux (schlieren), ou par des phénomènes d'érosion le long des surfaces de contact. Deux couches métriques à contour sinueux consistent en une accumulation compacte d'enclaves mafiques arrondies dans une matrice granodioritique fine. Le granoclassement des enclaves, la présence de figures de charge et de phénomènes érosifs en base de couche, ainsi que des schlieren de biotite entrecroisés évoquent l'injection de coulées de magma chargé d'enclaves et de faible viscosité en régime hydrodynamique turbulent dans un encaissant granodioritique encore largement liquide. La nature hybride des roches implique une chambre magmatique sous-jacente, en cours de différenciation et périodiquement réalimentée. Les magmas sont des liquides mafiques dérivés du manteau et des liquides anatectiques d'origine crustale, comme l'indique la gamme mesurée des rapports isotopiques initiaux du Sr (0.704 à 0.709) et des valeurs epsilon Nd (-2.1 à -4.7). Ces données montrent également que la contribution crustale est dominante, en accord avec les isotopes du plomb. Les phénomènes d'hybridation ont vraisemblablement eu lieu en base de croûte et dans la chambre magmatique sous-jacente au laccolite du Matorello. Les indicateurs de paléogravité du Matorello contribuent accessoirement à la compréhension de l'architecture actuelle de la nappe de Sambuco. Des plis isoclinaux à surface axiale verticale peuvent être mis en évidence par le contact entre les faciès dioritique et granodioritique. L'antiforme dont le Matorello forme le coeur est un synclinal, ce qui le positionne dans le Flanc inverse du grand pli couché que forme la nappe de Sambuco. Par ailleurs, des blocs de gneiss retrouvés dans le wildflysch sommital de la couverture de la nappe d'Antigorio ont été affiliés dans cette étude au pluton du Matorello. Ceci implique que le front de la nappe de Sambuco chevauchait déjà la partie est du bassin d'Antigorio au moment de sa fermeture. Par conséquent, ce n'est qu'en position externe que la nappe du Lebendun chevauche directement la nappe d'Antigorio. Abstract Magmatic bodies are important markers in paleo-geographic or geodynamic reconstructions of orogenic cycles, even more so in the case of polycyclic events where many of the other markers have been overwritten or destroyed. Plutons are relatively easy to date and their geochemical properties help constrain the tectonic context in which they were emplaced. This study focuses on the pre-mesozoic basement in the Sambuco and Maggia lower Penninic nappes located in the central Lepontine domain of the Alps. A number of magmatic events have been identified in the Sambuco basement. These events were dated using LA-ICPMS U/Pb on zircon grains. The mafic calc-alkaline banded Scheggia suite is dated as lower Cambrian, 540-530 Ma. The Al-rich Sasso-Nero lenticular gneiss is 480-470 Ma old (similarly to many older orfhogneisses of the Alpine basement) and contains 630-610 Ma old pan-African inherited zircons that illustrate the Gondwanian origin of these terranes.The calc-alkaline Matorello pluton is dated as 310-300 Ma whereas the lamprophyric bodies it contains are of 300 Ma. The Cocco granodiorite and the Ruscada leucogranite both intrude the basement of the adjacent Maggia nappe and are of similar ages to the Matorello. The ages as well as the geochemical similarities between the Cocco, Rucada and Matorello plutons suggest their paleo-geographic proximity at the Permian-Carboniferous boundary. However, these nappes are currently considered as belonging to two different Mesozoic paleo-geographic domains. Indeed, the Sambuco is considered as Helvetic whereas the Maggia is said to be Briançonnais, both separated by an oceanic basin. If this is the case, then it is essential that nostrike-slip movement has misaligned both continental margins since these coincide perfectly now that the oceanic domain closed. The Matorello pluton was originally a tabular intrusion, built up by the accumulation of multiple, several meter-thick, subhorizontal sheet-like injections of magma. Depending on their emplacement rate, the successive magma injections either solidified rapidly with sharp and rather well-defined boundaries (like the composite sills) or mingled with previous injections generating a thick molten layer up to several tens to hundred meters thick, like in the main granodioritic facies. These coalesced injections are hardly distinguishable, however subtle contrasts in granulometry, mineral modal proportions or mineral sorting (cross-bedded biotite-rich schlieren), as well as erosional features and/or crystal entrapment along contact surfaces allow to distinguish between the different injections. Two exceptional meter-thick layers display sinuous boundaries with the host granodiorite and consist of a densely packed accumulation of mafic enclaves in a granodioritic matrix. Gravitational sorting of the enclaves with load cast features at the base of the layers and sinuous biotite schlieren point to injection of low viscosity turbulent composite magma flows in the still largely molten granodiorite host. The hybrid nature of these rocks implies the existence of á periodically replenished and differentiated underlying magma chamber. Magmas are mafic liquids derived from the mantle and anatectic liquids of crustal origin, as shown by the (87Sr/86Sr), and epsilon Nd values (0.704-0.709 and -2.1 to -4.7 respectively. These data show that the crustal contribution is important, as confirmed by the Pb isotopes. The hybridisation processes seem to have occurred in the lower crust in magma chambers underlying the Matorello laccolith. The paleo-gravity markers in the Matorello help understand the architecture of the Sambuco nappe. Isoclinal folds with a vertical axial plane can be seen at the contact between dioritic and granodioritic facies. The antiform structure of which the Matorello is the heart is in fact a syncline. This places it in the inverse flanc of the large recumbent fold that constitutes the Sambuco nappe. The gneiss blocs found in the summital wildflysh cover of the Antigorio nappe have been linked to the Matorello pluton. This means that the front of the Sambuco nappe already overlapped the Antigorio basin when it closed. This implies that the Lebendun nappe can only overlap the Antigorio nappe in it's external position. Résumé grand public La chaîne alpine est la conséquence de la collision tertiaire entre deux masses continentales, l'Europe au nord et la péninsule apulienne africaine au sud, originellement séparées par l'océan mésozoïque téthysien. Cette collision a fermé un espace large de plusieurs centaines de km avec pour résultat l'écaillage de la croûte terrestre en unités tectoniques de dimensions variables, qui se sont empilées, imbriquées, éventuellement replissées en nappes de géométrie complexe. Cet amoncellement de 40 km d'épaisseur a vu sa température et sa pression lithostatique internes augmenter jusqu'à des valeurs de l'ordre de 680 °C et 6000 bars, induisant une recristallisation métamorphique des roches. L'un des objectifs de la géologie alpine est de reconstituer la géographie de la région aux temps mésozoïques de l'océan téthysien, en d'autres termes, de replacer chacune des unités tectoniques identifiées au sein de l'empilement alpin dans sa position originelle. Le défi est de taille et peut être comparé à celui de la reconstitution d'un vaste puzzle, dont certaines pièces seraient endommagées au niveau de leur contour ou leurs couleurs (métamorphisme), dissimulées par d'autres (enfouissement), voire tombées de la table de jeu (subduction, échappement latéral). Plusieurs approches ont été mises en oeuvre au cours du siècle écoulé. On citera en particulier la stratigraphie, la tectonique et le paléomagnétisme. Dans ce travail, nous avons essentiellement utilisé des techniques de datation isotopique absolue des roches (U/Pb sur zircon) qui, sur la base des connaissances acquises par l'ensemble des autres disciplines géologiques, nous ont permis de mieux contraindre ta paléogéographie mésozoïque du domaine «pennique inférieur » des Alpes centrales lépontines. Et au-delà? Nous savons tous que la disposition des continents à la surface de la Terre évolue constamment. Il est donc tentant d'essayer de remonter plus loin encore dans le temps et de reconstituer la physionomie de la marge sud européenne, tout au moins certains éléments de son histoire, au cours de l'ère paléozoïque. Les traces de ces événements très anciens sont naturellement ténues et dans ce contexte, les techniques de datation mentionnées ci-dessus deviennent les outils les plus performants. Ainsi, des datations u/Pb sur zircon nous ont permis de recenser plusieurs intrusions magmatiques, attribuées à quatre événements orogéniques anté-alpins. Des âges néoprotérozoïques (630-610 millions d'années ou Ma), cambrien inférieur (540-530 Ma), ordovicien inférieur (480-470 Ma) et carbonifère supérieur-permien inférieur (310-285 Ma) ont été obtenus dans le socle de la nappe de Sambuco. Des âges similaires à 300 Ma ont été obtenus dans la nappe voisine de la Maggia, qui permettent de relier ces deux unités. Aujourd'hui côte à côte, ces deux nappes devaient également se trouver proches l'une de l'autre il y a 300 Ma, lors de l'extension post-varisque. Les structures magmatiques spectaculaires préservées dans le pluton du Matorello (300 Ma) contraignent la géométrie actuelle de la nappe de Sambuco dans laquelle l'intrusion s'est mise en place. La forme originelle du pluton, aujourd'hui retourné et replissé plusieurs fois, s'avère être tabulaire, faite d'intrusions de faible épaisseur (1-300 m) s'étalant en forme de disque (30m à 2 km de diamètre). Les injections successives de magma se sont accumulées sous un toit dioritique précoce; elles sont issues, par le refais de fractures, d'une chambre magmatique plus profonde, périodiquement réalimentée par des magmas calco-alcalins d'origine mantellique contaminés parla croûte continentale profonde (εNd = -2.1 à -4.7). Des accumulations d'enclaves magmatiques arrondies et granoclassées dans des paléo-chenaux à fond érosif témoignent de conditions de mise en place hydrodynamiques à haute énergie. Ces enclaves sont emmenées de la chambre magmatique sous-jacente à la faveur d'épisodes de fracturation hydraulique liés à l'injection de magmas matelliques chauds dans des liquides différenciés riches en eau. Cette hypothèse est étayée par l'existence de filons composites. Une paléohorizontale a pu être déduite au sein du pluton, indiquant que cette partie de la nappe de Sambuco est verticalisée et isoclinalement replissée par la déformation alpine. Finalement, des blocs érodés du socle Sambuco ont été retrouvés dans le wildflysch sommital de la couverture sédimentaire mésozoïque de la nappe d'Antigorio sous-jacente. Ceci suggère que les blocs ont été fournis parle front de la nappe de Sambuco en train de chevaucher sur la nappe d'Antigorio au moment de la fermeture du bassin sédimentaire de cette dernière.

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.

Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps

The role of competition for light among plants has long been recognized at local scales, but its potential importance for plant species' distribution at larger spatial scales has largely been ignored. Tree cover acts as a modulator of local abiotic conditions, notably by reducing light availability below the canopy and thus the performance of species that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains. Using 6,935 vegetation plots located across the European Alps, we fit Generalized Linear Models (GLM) for the distribution of 960 herbs and shrubs species to assess the effect of tree cover at both plot and landscape grain sizes (~ 10-m and 1-km, respectively). We ran four models with different combinations of variables (climate, soil and tree cover) for each species at both spatial grains. We used partial regressions to evaluate the independent effects of plot- and landscape-scale tree cover on plant communities. Finally, the effects on species' elevational range limits were assessed by simulating a removal experiment comparing the species' distribution under high and low tree cover. Accounting for tree cover improved model performance, with shade-tolerant species increasing their probability of presence at high tree cover whereas shade-intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both plot and landscape spatial grains, albeit strongest at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot-scale plant communities, suggesting that the effects may be transmitted to coarser grains through meta-community dynamics. At high tree cover, shade-intolerant species exhibited elevational range contractions, especially at their upper limit, whereas shade-tolerant species showed elevational range expansions at both limits. Our findings suggest that the range shifts for herb and shrub species may be modulated by tree cover dynamics.

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.

Coarse-graining and thermodynamics in far-from-equilibrium systems

Lying at the core of statistical physics is the need to reduce the number of degrees of freedom in a system. Coarse-graining is a frequently-used procedure to bridge molecular modeling with experiments. In equilibrium systems, this task can be readily performed; however in systems outside equilibrium, a possible lack of equilibration of the eliminated degrees of freedom may lead to incomplete or even misleading descriptions. Here, we present some examples showing how an improper coarse-graining procedure may result in linear approaches to nonlinear processes, miscalculations of activation rates and violations of the fluctuation-dissipation theorem.

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.