Estabilitat i diagènesis dels fitòlits de silici en els jaciments arqueològics

Estudi realitzat a partir d’una estada al Kimmel Center for Archaeological Research, Israel, entre 2010 i 2012. Els fitòlits són un dels components principals dels sediments arqueològics. Són relativament estables i menys propensos a la degradació biològica que altres restes vegetals, però també poden ser afectats per la diagènesis. Per entendre com la diagènesis afecta als fitòlits hem desenvolupat una aproximació experimental utilitzant solucions alcalines per determinar l’estabilitat individual de fitòlits fòssils i moderns. L’experimentació ha estat completada amb un estudi de camp a Izbet Sartah. Els resultats mostren com la diagènesis canvia la composició dels conjunts de fitòlits, i per tant afecta la interpretació arqueològica. Conseqüentment, hem desenvolupat un mètode per determinar l’estat de preservació dels fitòlits en els jaciments arqueològics. L’experimentació mostra com els fitòlits moderns són més solubles que els fitòlits fòssils. Tant els fitòlits fòssils com els moderns són menys estables si són cremats. No totes les morfologies es preserven igual, indicant així que hi ha unes morfologies més estables que unes altres. Els fitòlits amb decoracions delicades, especialment aquells formats a la inflorescència de gramínies, són més propensos a la dissolució que els de les fulles. L’avaluació de l’estat de preservació dels fitòlits en jaciments arqueològics es pot realitzar utilitzant un conjunt de tècniques com ara: l’Index de Variació de Fitòlits, el mètode de dissolució ràpida, la identificació de morfologies delicades i la utilització del FTIR. Proposem que la diagènesis dels fitòlits depèn directament de la quantitat inicial de fitòlits en els sediments, la velocitat de sedimentació, i la presència o absència de fitòlits i plantes modernes en l’àrea estudiada. Els resultats d’aquesta investigació han estat publicats en dos articles afegits al final de l’informe (Cabanes et al., 2011 i Cabanes et al., in press), presentats en congressos internacionals i utilitzats indirectament en altres investigacions.

Bristle pattern formation in the thorax formation of Drosophila: a systems level approach

A fundamental question in developmental biology is how tissues are patterned to give rise to differentiated body structures with distinct morphologies. The Drosophila wing disc offers an accessible model to understand epithelial spatial patterning. It has been studied extensively using genetic and molecular approaches. Bristle patterns on the thorax, which arise from the medial part of the wing disc, are a classical model of pattern formation, dependent on a pre-pattern of trans-activators and –repressors. Despite of decades of molecular studies, we still only know a subset of the factors that determine the pre-pattern. We are applying a novel and interdisciplinary approach to predict regulatory interactions in this system. It is based on the description of expression patterns by simple logical relations (addition, subtraction, intersection and union) between simple shapes (graphical primitives). Similarities and relations between primitives have been shown to be predictive of regulatory relationships between the corresponding regulatory factors in other Systems, such as the Drosophila egg. Furthermore, they provide the basis for dynamical models of the bristle-patterning network, which enable us to make even more detailed predictions on gene regulation and expression dynamics. We have obtained a data-set of wing disc expression patterns which we are now processing to obtain average expression patterns for each gene. Through triangulation of the images we can transform the expression patterns into vectors which can easily be analysed by Standard clustering methods. These analyses will allow us to identify primitives and regulatory interactions. We expect to identify new regulatory interactions and to understand the basic Dynamics of the regulatory network responsible for thorax patterning. These results will provide us with a better understanding of the rules governing gene regulatory networks in general, and provide the basis for future studies of the evolution of the thorax-patterning network in particular.

Investigation and monitoring of rock slope instabilities in Norway by terrestrial laser scanning

Long-range Terrestrial Laser Scanning (TLS) is widely used in studies on rock slope instabilities. TLS point clouds allow the creation of high-resolution digital elevation models for detailed mapping of landslide morphologies and the measurement of the orientation of main discontinuities. Multi-temporal TLS datasets enable the quantification of slope displacements and rockfall volumes. We present three case studies using TLS for the investigation and monitoring of rock slope instabilities in Norway: 1) the analysis of 3D displacement of the Oksfjellet rock slope failure (Troms, northern Norway); 2) the detection and quantification of rockfalls along the sliding surfaces and at the front of the Kvitfjellet rock slope instability (Møre og Romsdal, western Norway); 3) the analysis of discontinuities and rotational movements of an unstable block at Stampa (Sogn og Fjordane, western Norway). These case studies highlight the possibilities but also limitations of TLS in investigating and monitoring unstable rock slopes.

Spatial pattern of floral morphology: a possible insight into the effects of pollinators on plant distribution

Pollination syndromes involve convergent evolution towards phenotypes composed of specific scents, colours or floral morphologies that attract or restrict pollinator access to reward. How these traits might influence the distributions of plant species in interaction with pollinators has rarely been investigated. We sampled 870 vegetation plots in the western Swiss Alps and classified the plant species into seven blossom types according to their floral morphology (wind, disk, funnel, tube, bilabiate, head or brush). We investigated the environmental features of plots with functional diversity (FD) lower than expected by chance alone to detect potential pollination filtering and related the proportions of the seven blossom types to a combination of environmental descriptors. From these results, we inferred the potential effect of the pollinator on the spatial distribution of plant species. The vegetation plots with significantly lower FD of blossom types than expected by chance were found at higher altitudes, and the proportions of blossom types were strongly patterned along the same gradient. These results support a biotic filtering effect on plant species assemblages through pollination: disk blossoms became dominant at higher altitudes, resulting in a lower FD. In harsh conditions at high altitudes, pollinators usually decrease in activity, and the openness of the disk blossom grants access to any available pollinator. Inversely, bilabiate blossoms, which are mostly pollinated by bees, were more abundant at lower elevations, which are characterised by greater abundance and diversity of bees. Generalisation through openness of the blossom could be advantageous at high elevations, while specialisation could be a successful alternative strategy at lower elevations. The approach used in this study is purely correlative, and further investigations should be conducted to infer the nature of the causal relationship between plant and pollinator distributions.

Comparative description of the immature stages of two very similar leaf footed bugs, Holymenia clavigera (Herbst) and Anisoscelis foliacea marginella (Dallas) (Hemiptera, Coreidae, Anisoscelini)

Holymenia clavigera (Herbst, 1784) and Anisoscelis foliacea marginella (Dallas, 1852) (Hemiptera, Coreidae) present a remarkable similarity regarding egg and nymphal morphology. On the contrary, their adult stages are remarkably different. This study describes and compares the immature stages of these two coreid species. Excepting for the last instar and the shape of the hind tibia from third to last instar, nymphs of both species were identical in their gross morphologies and ultrastructures. However, H. clavigera was significantly larger than A. foliacea marginella in all stages. Thus, we suggest that these species may have evolved through evolutionary convergence, parsimony between the immature stages after speciation, Müllerian mimicry or genetic drift.

Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009

Different types of cell death are often defined by morphological criteria, without a clear reference to precise biochemical mechanisms. The Nomenclature Committee on Cell Death (NCCD) proposes unified criteria for the definition of cell death and of its different morphologies, while formulating several caveats against the misuse of words and concepts that slow down progress in the area of cell death research. Authors, reviewers and editors of scientific periodicals are invited to abandon expressions like 'percentage apoptosis' and to replace them with more accurate descriptions of the biochemical and cellular parameters that are actually measured. Moreover, at the present stage, it should be accepted that caspase-independent mechanisms can cooperate with (or substitute for) caspases in the execution of lethal signaling pathways and that 'autophagic cell death' is a type of cell death occurring together with (but not necessarily by) autophagic vacuolization. This study details the 2009 recommendations of the NCCD on the use of cell death-related terminology including 'entosis', 'mitotic catastrophe', 'necrosis', 'necroptosis' and 'pyroptosis'.

El modelat del massís de Begur

In the present paper, the diverse morphologies observed in the Begur Mountain Range are described and the controlling development factors and their relationships are analized. Finally, a systematics of the different rock types macro and microforms is presented

Crescent and star shapes of members of the Chlamydiales order: impact of fixative methods.

Members of the Chlamydiales order all share a biphasic lifecycle alternating between small infectious particles, the elementary bodies (EBs) and larger intracellular forms able to replicate, the reticulate bodies. Whereas the classical Chlamydia usually harbours round-shaped EBs, some members of the Chlamydia-related families display crescent and star-shaped morphologies by electron microscopy. To determine the impact of fixative methods on the shape of the bacterial cells, different buffer and fixative combinations were tested on purified EBs of Criblamydia sequanensis, Estrella lausannensis, Parachlamydia acanthamoebae, and Waddlia chondrophila. A linear discriminant analysis was performed on particle metrics extracted from electron microscopy images to recognize crescent, round, star and intermediary forms. Depending on the buffer and fixatives used, a mixture of alternative shapes were observed in varying proportions with stars and crescents being more frequent in C. sequanensis and P. acanthamoebae, respectively. No tested buffer and chemical fixative preserved ideally the round shape of a majority of bacteria and other methods such as deep-freezing and cryofixation should be applied. Although crescent and star shapes could represent a fixation artifact, they certainly point towards a diverse composition and organization of membrane proteins or intracellular structures rather than being a distinct developmental stage.

Nucleation and growth of GaN nanorods on Si (111) surfaces by plasma-assisted molecular beam epitaxy - The influence of Si- and Mg-doping

The self-assembled growth of GaN nanorods on Si (111) substrates by plasma-assisted molecular beam epitaxy under nitrogen-rich conditions is investigated. An amorphous silicon nitride layer is formed in the initial stage of growth that prevents the formation of a GaN wetting layer. The nucleation time was found to be strongly influenced by the substrate temperature and was more than 30 min for the applied growth conditions. The observed tapering and reduced length of silicon-doped nanorods is explained by enhanced nucleation on nonpolar facets and proves Ga-adatom diffusion on nanorod sidewalls as one contribution to the axial growth. The presence of Mg leads to an increased radial growth rate with a simultaneous decrease of the nanorod length and reduces the nucleation time for high Mg concentrations.

Ontogeny and covariation in the Toarcian genus Osperleioceras (Ammonoidea)

Starting from embryonic (protoconch-ammonitella) and early juvenile shells, which are indistinguishable at the species level, growth curves of Osperleioceras from the Reynesi Subzone (Upper Toarcian) of the Causses Basin (Aveyron, France) show a continuous radiating range of correlated variation in dimensional and ornamental characters, such as involution, whorl compression, rib strength and rib density. This covariation pattern can be observed among single-horizon assemblages, as well as during individual ontogenetic development. The existence of a continuous intergradational series of shells, ranging from stout coarsely ribbed to smooth suboxycone morphologies, rules out functional or ecological selectivity to explain this non-random variability pattern. The complex interdependence of shape and sculpture can be simulated by a model in which sculpture intensity depends on mantle curvature [GUEX, 1999]. The expression of covariation in subadult specimens since the base of Upper Toarcian reveals a rise in variability, concomitant with a size decrease, both contemporaneous with environmental instability. It developed in successive bursts from a fairly long low variability period spanning the whole Middle Toarcian.

Pattern formation during mesophase growth in a homologous series

Remarkable differences in the shape of the nematic-smectic-B interface in a quasi-two-dimensional geometry have been experimentally observed in three liquid crystals of very similar molecular structure, i.e., neighboring members of a homologous series. In the thermal equilibrium of the two mesophases a faceted rectanglelike shape was observed with considerably different shape anisotropies for the three homologs. Various morphologies such as dendritic, dendriticlike, and faceted shapes of the rapidly growing smectic-B germ were also observed for the three substances. Experimental results were compared with computer simulations based on the phase field model. The pattern forming behavior of a binary mixture of two homologs was also studied.

Geometric morphometric analyses provide evidence for the adaptive character of the Tanganyikan cichlid fish radiations.

The cichlids of East Africa are renowned as one of the most spectacular examples of adaptive radiation. They provide a unique opportunity to investigate the relationships between ecology, morphological diversity, and phylogeny in producing such remarkable diversity. Nevertheless, the parameters of the adaptive radiations of these fish have not been satisfactorily quantified yet. Lake Tanganyika possesses all of the major lineages of East African cichlid fish, so by using geometric morphometrics and comparative analyses of ecology and morphology, in an explicitly phylogenetic context, we quantify the role of ecology in driving adaptive speciation. We used geometric morphometric methods to describe the body shape of over 1000 specimens of East African cichlid fish, with a focus on the Lake Tanganyika species assemblage, which is composed of more than 200 endemic species. The main differences in shape concern the length of the whole body and the relative sizes of the head and caudal peduncle. We investigated the influence of phylogeny on similarity of shape using both distance-based and variance partitioning methods, finding that phylogenetic inertia exerts little influence on overall body shape. Therefore, we quantified the relative effect of major ecological traits on shape using phylogenetic generalized least squares and disparity analyses. These analyses conclude that body shape is most strongly predicted by feeding preferences (i.e., trophic niches) and the water depths at which species occur. Furthermore, the morphological disparity within tribes indicates that even though the morphological diversification associated with explosive speciation has happened in only a few tribes of the Tanganyikan assemblage, the potential to evolve diverse morphologies exists in all tribes. Quantitative data support the existence of extensive parallelism in several independent adaptive radiations in Lake Tanganyika. Notably, Tanganyikan mouthbrooders belonging to the C-lineage and the substrate spawning Lamprologini have evolved a multitude of different shapes from elongated and Lamprologus-like hypothetical ancestors. Together, these data demonstrate strong support for the adaptive character of East African cichlid radiations.

Topographic forcing of flow partition and flow structures at river bifurcations

This paper presents the predicted flow dynamics from the application of a Reynolds-averaged NavierStokes model to a series of bifurcation geometries with morphologies measured during previous flume experiments. The topography of the bifurcations consists of either plane or bedform-dominated beds which may or may not possess discordance between the two bifurcation distributaries. Numerical predictions are compared with experimental results to assess the ability of the numerical model to reproduce the division of flow into the bifurcation distributaries. The hydrodynamic model predicts: (1) diverting fluxes in the upstream channel which direct water into the distributaries; (2) super-elevation of the free surface induced at the bifurcation edge by pressure differences; and (3) counter-rotating secondary circulation cells which develop upstream of the apex of the bifurcation and move into the downstream channels, with water converging at the surface and diverging at the bed. When bedforms are not present, weak transversal fluxes characterize the upstream channel for almost its entire length, associated with clearly distinguishable secondary circulation cells, although these may be under-estimated by the turbulence model used in the solution. In the bedform dominated case, the same hydrodynamic conditions were not observed, with the bifurcation influence restricted and depth scale secondary circulation cells not forming. The results also demonstrate the dominant effect bed discordance has upon flow division between the two distributaries. Finally, results indicate that in bedform dominated rivers. Consequently, we suggest that sand-bed river bifurcations are more likely to have an influence that extends much further upstream and have a greater impact upon water distribution. This may contribute to observed morphological differences between sand-bedded and gravel-bedded braided river networks. Copyright (C) 2012 John Wiley & Sons, Ltd.

Job switching in ants: role of a kinase

Reproductive division of labour is a defining characteristic of eusociality in insect societies. The task of reproduction is performed by the fertile males and queens of the colony, while the non-fertile female worker caste performs all other tasks related to colony upkeep, foraging and nest defence. Division of labour, or polyethism, within the worker caste is organized such that specific tasks are performed by discrete groups of individuals. Ordinarily, workers of one group will not participate in the tasks of other groups making the groups of workers behaviourally distinct. In some eusocial species, this has led to the evolution of a remarkable diversity of subcaste morphologies within the worker caste, and a division of labour amongst the subcastes. This caste polyethism is best represented in many species of ants where a smaller-bodied minor subcaste typically performs foraging duties while larger individuals of the major subcaste are tasked with nest defence. Recent work suggests that polyethism in the worker caste is influenced by an evolutionarily conserved, yet diversely regulated, gene called foraging (for), which encodes a cGMP-dependent protein kinase (PKG). Additionally, flexibility in the activity of this enzyme allows for workers from one task group to assist the workers of other task groups in times of need during the colony's life.

Budgeting rockfall and modeling sedimentary delivery in torrent systems

This thesis is a compilation of projects to study sediment processes recharging debris flow channels. These works, conducted during my stay at the University of Lausanne, focus in the geological and morphological implications of torrent catchments to characterize debris supply, a fundamental element to predict debris flows. Other aspects of sediment dynamics are considered, e.g. the coupling headwaters - torrent, as well as the development of a modeling software that simulates sediment transfer in torrent systems. The sediment activity at Manival, an active torrent system of the northern French Alps, was investigated using terrestrial laser scanning and supplemented with geostructural investigations and a survey of sediment transferred in the main torrent. A full year of sediment flux could be observed, which coincided with two debris flows and several bedload transport events. This study revealed that both debris flows generated in the torrent and were preceded in time by recharge of material from the headwaters. Debris production occurred mostly during winter - early spring time and was caused by large slope failures. Sediment transfers were more puzzling, occurring almost exclusively in early spring subordinated to runoffconditions and in autumn during long rainfall. Intense rainstorms in summer did not affect debris storage that seems to rely on the stability of debris deposits. The morpho-geological implication in debris supply was evaluated using DEM and field surveys. A slope angle-based classification of topography could characterize the mode of debris production and transfer. A slope stability analysis derived from the structures in rock mass could assess susceptibility to failure. The modeled rockfall source areas included more than 97% of the recorded events and the sediment budgets appeared to be correlated to the density of potential slope failure. This work showed that the analysis of process-related terrain morphology and of susceptibility to slope failure document the sediment dynamics to quantitatively assess erosion zones leading to debris flow activity. The development of erosional landforms was evaluated by analyzing their geometry with the orientations of potential rock slope failure and with the direction of the maximum joint frequency. Structure in rock mass, but in particular wedge failure and the dominant discontinuities, appear as a first-order control of erosional mechanisms affecting bedrock- dominated catchment. They represent some weaknesses that are exploited primarily by mass wasting processes and erosion, promoting not only the initiation of rock couloirs and gullies, but also their propagation. Incorporating the geological control in geomorphic processes contributes to better understand the landscape evolution of active catchments. A sediment flux algorithm was implemented in a sediment cascade model that discretizes the torrent catchment in channel reaches and individual process-response systems. Each conceptual element includes in simple manner geomorphological and sediment flux information derived from GIS complemented with field mapping. This tool enables to simulate sediment transfers in channels considering evolving debris supply and conveyance, and helps reducing the uncertainty inherent to sediment budget prediction in torrent systems. Cette thèse est un recueil de projets d'études des processus de recharges sédimentaires des chenaux torrentiels. Ces travaux, réalisés lorsque j'étais employé à l'Université de Lausanne, se concentrent sur les implications géologiques et morphologiques des bassins dans l'apport de sédiments, élément fondamental dans la prédiction de laves torrentielles. D'autres aspects de dynamique sédimentaire ont été abordés, p. ex. le couplage torrent - bassin, ainsi qu'un modèle de simulation du transfert sédimentaire en milieu torrentiel. L'activité sédimentaire du Manival, un système torrentiel actif des Alpes françaises, a été étudiée par relevés au laser scanner terrestre et complétée par une étude géostructurale ainsi qu'un suivi du transfert en sédiments du torrent. Une année de flux sédimentaire a pu être observée, coïncidant avec deux laves torrentielles et plusieurs phénomènes de charriages. Cette étude a révélé que les laves s'étaient générées dans le torrent et étaient précédées par une recharge de débris depuis les versants. La production de débris s'est passée principalement en l'hiver - début du printemps, causée par de grandes ruptures de pentes. Le transfert était plus étrange, se produisant presque exclusivement au début du printemps subordonné aux conditions d'écoulement et en automne lors de longues pluies. Les orages d'été n'affectèrent guère les dépôts, qui semblent dépendre de leur stabilité. Les implications morpho-géologiques dans l'apport sédimentaire ont été évaluées à l'aide de MNT et études de terrain. Une classification de la topographie basée sur la pente a permis de charactériser le mode de production et transfert. Une analyse de stabilité de pente à partir des structures de roches a permis d'estimer la susceptibilité à la rupture. Les zones sources modélisées comprennent plus de 97% des chutes de blocs observées et les bilans sédimentaires sont corrélés à la densité de ruptures potentielles. Ce travail d'analyses des morphologies du terrain et de susceptibilité à la rupture documente la dynamique sédimentaire pour l'estimation quantitative des zones érosives induisant l'activité torrentielle. Le développement des formes d'érosion a été évalué par l'analyse de leur géométrie avec celle des ruptures potentielles et avec la direction de la fréquence maximale des joints. Les structures de roches, mais en particulier les dièdres et les discontinuités dominantes, semblent être très influents dans les mécanismes d'érosion affectant les bassins rocheux. Ils représentent des zones de faiblesse exploitées en priorité par les processus de démantèlement et d'érosion, encourageant l'initiation de ravines et couloirs, mais aussi leur propagation. L'incorporation du control géologique dans les processus de surface contribue à une meilleure compréhension de l'évolution topographique de bassins actifs. Un algorithme de flux sédimentaire a été implémenté dans un modèle en cascade, lequel divise le bassin en biefs et en systèmes individuels répondant aux processus. Chaque unité inclut de façon simple les informations géomorpologiques et celles du flux sédimentaire dérivées à partir de SIG et de cartographie de terrain. Cet outil permet la simulation des transferts de masse dans les chenaux, considérants la variabilité de l'apport et son transport, et aide à réduire l'incertitude liée à la prédiction de bilans sédimentaires torrentiels. Ce travail vise très humblement d'éclairer quelques aspects de la dynamique sédimentaire en milieu torrentiel.