Évolution biologique et ADN ancien

Après deux décennies de découvertes et de controverses, la paléogénétique semble, sinon avoir atteint l’âge de raison, du moins avoir délaissé les frasques de son impétueuse jeunesse. Si ses principes théoriques ont été à peine affinés en quinze ans, sa pratique opérationnelle a, elle, rapidement évolué, en bénéficiant de l’explosion méthodologique de la biologie moléculaire. C’est véritablement avec l’avènement de la méthode d’amplification de l’ADN par PCR que ce champ d’étude a pris son essor. Dès 1989, les travaux se multipliaient en s’intéressant à des groupes biologiques animaux et végétaux variés : espèces récemment éradiquées par l’homme (ratites), représentants disparus de la période glaciaire (mammouth laineux) ou, encore, espèces domestiques (cochon) définirent les entités qui restent aujourd’hui les cibles favorites de ces études. Les champs d’application se sont également multipliés, afin de mieux cerner l’évolution des espèces, des populations et des génomes : génétique des populations, phylogénie d’espèces, domestication, migration de populations, paléopathologie, paléogénomique et évolution moléculaire s’offrent désormais à une discipline décidément en plein essor.Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology discipline

Determination of the components of the gyration tensor of quartz by oblique incidence transmission two-modulator generalized ellipsometry

The two independent components of the gyration tensor of quartz, g11 and g33, have been spectroscopically measured using a transmission two-modulator generalized ellipsometer. The method is used to determine the optical activity in crystals in directions other than the optic axis, where the linear birefringence is much larger than the optical activity

Structure vs. excitonic transitions in self-assembled porphyrin nanotubes and their effect on light absorption and scattering

The optical properties of diprotonated meso-tetrakis(4-sulphonatophenyl)porphyrin (TPPS4) J-aggregates of elongated thin particles (nanotubes in solution and ribbons when deposited on solid interfaces) are studied by different polarimetric techniques. The selective light extinction in these structures, which depends on the alignment of the nanoparticle with respect to the polarization of light, is contributed by excitonic absorption bands and by resonance light scattering. The optical response as a function of the polarization of light is complex because, although the quasi-one-dimensional structure confines the local fields along the nanotube axis, there are two orthogonal excitonic bands, of H- and J-character, that can work in favor of or against the field confinement. Results suggest that resonance light scattering is the dominant effect in solid state preparations, i.e. in collective groups (bundles) of ribbons but in diluted solutions, i.e. with isolated nanotubes, the absorption at the excitonic transitions remains dominant and linear dichroism spectra can be a direct probe of the exciton orientations. Therefore, by analyzing scattering and absorption data we can determine the alignment of the excitonic bands within the nanoparticle, i.e. of the orientation of the basic 2D porphyrin architecture in the nanoparticle. This is a necessary first step for understanding the directions of energy transport, charge polarization and non-linear optical properties in these materials

Mueller matrix polarimetry of anisotropic chiral media

[eng] Esta tesis se centra en el estudio de medios quirales mediante polarimetría de matriz de Mueller. Ópticamente los medios quirales se caracterizan por tener actividad óptica, que se manifiesta en procesos dispersivos con la birefringencia circular o en procesos de absorción mediante el cicroismo circular. Nuestro ámbito de estudio han estado los anisótropos no es posible aplicar los métodos convencionales de determinación de la actividad óptica ya que la descripción de la propagación de la luz polarizada se vuelve mucho más compleja ya que el dicroismo y la birefringencia lineales también están presentes. Una parte importante del trabajo han sido el desarrollo teórico necesario para poder obtener los parámetros de dicroismo circular o birefringencia circular a partir de las medidas de la Matriz de Mueller de una muestra anisótropa arbitraria. Otra parte importante del trabajo ha sido la y construcción de un polarímetro de matriz de Mueller de alta resolución basado en el uso de dos moduladores fotoelásticos y es capaz de trabajar en dos modos de funcionamiento: espectroscópico y con resolución espacial. Los desarrollos instrumentales teórico nos han llevado a poder realizar caracterizar muestras de diversa índole. En el ámbito cristalográfico hemos medido espectroscópicamente el tensor de girotropía del cuarzo y hemos mostrado la posibilidad de distinguir dominios quirales en capas delgadas policristalinas. Otro apartado experimental fundamental ha sido la caracterización de procesos de inducción de quiralidad supramolecular mediante efectos hidrodinámicos en soluciones agitadas de nanopartículas orgánicas de formas alargadas

Relation between 2D/3D chirality and the appearence of chiroptical effects in real nanostructures.

The optical activity of fabricated metallic nanostructures is investigated by complete polarimetry. While lattices decorated with nanoscale gammadia etched in thin metallic films have been described as two dimensional, planar nanostructures, they are better described as quasi-planar structures with some three dimensional character. We find that the optical activity of these structures arises not only from the dissymmetric backing by a substrate but, more importantly, from the selective rounding of the nanostructure edges. A true chiroptical response in the far-field is only allowed when the gammadia contain these non-planar features. This is demonstrated by polarimetric measurements in conjunction with electrodynamical simulations based on the discrete dipole approximation that consider non-ideal gammadia. It is also shown that subtle planar dissymmetries in gammadia are sufficient to generate asymmetric transmission of circular polarized light

Spectroscopic ellipsometry of very rough surfaces

This work expands the use of spectroscopic ellipsometry to surfaces with roughness that is similar to or larger than the wavelength of the incident light. By using a custom-built spectroscopic ellipsometer and varying the angle of incidence, we were able to differentiate between the diffusely scattered and specularly reflected components. Our findings demonstrate that measuring the diffuse component at specular angles is highly beneficial for ellipsometry analysis, as its response is equivalent to that of a smooth material. This allows for accurate determination of the optical constants in materials with extremely rough surfaces. Our results have the potential to broaden the scope and utility of the spectroscopic ellipsometry technique

Geometrical Phase Optical Components: Measuring Geometric Phase without Interferometry

Optical components that are based on Pancharatnam-Berry phase feature a polarization-dependent diffraction that can be used to fabricate lenses and gratings with unique properties. In recent years, the great progress made in the fabrication of the metasurfaces that are required for these optical components has lowered their cost and has made them widely available. One of the often-overlooked properties of optical components based on geometrical phases (GPs) is that, contrary to dynamical phases, their phase can be measured while using a polarimetric technique without the need to resort to interferometry methods. This is possible because the Pancharatnam-Berry phase is not controlled by an optical path difference; it results from a space variant polarization manipulation. In this work, we apply Mueller matrix microscopy in order to measure the geometrical phase of GP lenses and polarization gratings. We show that a single space resolved Mueller matrix measurement with micrometric resolution is enough to obtain a full characterization phase-profile of these GP-based optical components and evaluate their performance

Asymmetric Scattering and Reciprocity in a Plasmonic Dimer

We study the scattering of polarized light by two equal corner stacked Au nanorods that exhibit strong electromagnetic coupling. In the far field, this plasmonic dimer manifests very prominent asymmetric scattering in the transverse direction. Calculations based on a system of two coupled oscillators, as well as simulations based on the boundary element method, show that, while in one configuration both vertical and horizontal polarization states are scattered to the detector, when we interchange the source and the detector, the scattered intensity of the horizontal polarization drops to zero. Following Perrin's criterion, it can be shown that this system, as well as any other linear system not involving magneto-optical effects, obeys the optical reciprocity principle. We show that the optical response of the plasmonic dimer, while preserving electromagnetic reciprocity, can be used for the non-reciprocal transfer of signals at a subwavelength scale

Anisotropic integral decomposition of depolarizing Mueller matrices

We propose a novel, computationally efficient integral decomposition of depolarizing Mueller matrices allowing for the obtainment of a nondepolarizing estimate, as well as for the determination of the elementary polarization properties, in terms of mean values and variancescovariances of their fluctuations, of a weakly anisotropic depolarizing medium. We illustrate the decomposition on experimental examples and compare its performance to those of alternative decomposition