Axolotl uniquely generates blastema cells as a pool of progenitor/stem cells to restore an entire limb, a particular property that other organisms, such as humans, do not have. What underlies these differences? Is the main difference that cells residing at the amputation plane (in the stump) undergo reprogramming processes to re-enter the embryonic program, which allows developmental patterning to start, or are there fundamental differences? There is also a significant debate about whether regeneration occurs via stem cell differentiation or by dedifferentiation of mature limb tissue. The aim of my thesis was to address following questions: Are the cells in the blastema reprogrammed or differentiated to regenerate? Are the blastema cells genetically reactivated de novo during regeneration? How does the amputated limb exactly know which part of the limb needs to be regenerate? Using a novel technique of long-term genetic fate mapping, my team demonstrated that dedifferentiation in regenerated axolotl muscle tissue does not occur. Instead, PAX7+ satellite cells indeed play an important role during muscle regeneration in the axolotl limb. Surprisingly, this is in contrast to the newt, which regenerates muscle cells through a dedifferentiation process. Therefore, there is a fundamental difference that underlies the regenerative mechanism ((Sandoval-Guzman et al., 2014) [KR1]). This demonstrates that there is an unexpected diversity and flexibility of cellular mechanims used during limb regeneration, even among two closely related species. Finally, if one salamander species uses a mammalian regenerative strategy (Cornelison and Wold, 1997; Collins et al., 2005) involving stem cells and another uses a dedifferentiative strategy, this raises the question of whether there are other fundamental aspects of regeneration that could also be anomalous. This hypothesis is promising since there could be more than one possible mechanism to induce mammalian regeneration. The process of limb regeneration in principle seems to be more similar to those of limb development as historically assumed. We showed molecularly that embryonic players are reused during regeneration by reactivating the position- and tissue-specific developmental gene programs by using the newly isolated Twist sequences as early blastema cell markers ((Kragl et al., 2013) [KR2]). To gain insights into the molecular mechanisms of the P/D limb patterning in general, it was crucial to study the early patterning events of the resident progenitor/stem cells by using the specific blastema cell marker HoxA as a positional marker along the proximo-distal axis. Our HOXA protein analysis using high molecular and cellular resolution as well as transplantation assays demonstrated for the first time that axolotl limb blastema cells acquire their positional identity in a proximal to distal sequence. We found a hierarchy of cellular restrictions in positional identities. Amputation at the level of the upper arm showed that the blastema harbors cells, which convert to lower arm and hand. We observed ((Roensch et al., 2013) [KR3]) for the first time that intercalation- the intermediate element (lower arm) arises later from an interaction between the proximal and distal cells identities- does not occur. Intercalation, which has been an accepted model for a long time, is not the patterning mechanism underlying normal (without any manipulation) limb regeneration that is unique to axolotl. We further demonstrated, using the Hox genes as markers that positional identity is cell-type specific since their effects were confirmed to be present in the lateral plate mesoderm- derived cells of the limb. As our knowledge about limb blastemas expands concerning cell composition and molecular events controlling patterning, the similarity to development is becoming more and more clear. My work has resolved many ambiguities surrounding the molecularly identification of different types of blastema cells and how P/D limb patterning occurs during regeneration in comparison to development. It has highlighted the importance of combining high-resolution methods, such as in situ hybridizations, single-cell PCR (sc-PCR) of individual dissociated blastema cells and genetic labeling methods with grafting experiments to map cell fates in vivo. In addition to understanding the processes of regeneration, another long-term goal in the regenerative medicine field is to identify key molecules that trigger the regeneration of tissues. Recently, my colleague Takuji Sugiura (Sugiura et al., 2016) observed that an early event of blastema formation is the secretion of molecules like MLP (MARCKS-like protein), which induces wound-associated cell cycle re-entry. Such findings further increase the enthusiasm of biologists to understand the underlying principles of regeneration. By building our knowledge of the molecules and pathways that are involved in tissue regeneration, we increase the possibility of identifying a way to ‘activate’ regenerative processes in humans and thus reach the final goal of regenerative medicine, which is to use the concepts of cellular reprogramming, stem cell biology and tissue engineering to repair complex body structures.

The main aim of this thesis was to investigate the occurrence of dolphins in Pacific waters adjacent to the Panama Canal in the context of biological, temporal and spatial factors. Acoustic data were collected at 101 sites at a range of distances and depths from the shipping region. Data were collected between March 2010 and April 2011 in a diurnal cycle over a total of 114 recording days. Received sound levels were split into 1/3 Octave bandwidths to study variation in sound pressure levels and then converted to spectrum density levels to show the sound components of the background noise in this region. Generalised Linear Models were used to relate dolphin whistle detections to temporal, spatial, environmental and acoustic variables. The major sources of background noise were biological noise from soniferous fish and snapping shrimp and anthropogenic noise from vessels characterised by mid to high frequencies produced by artisanal fishing boats. There was monthly and diurnal variation with some locations characterised by loud sounds in the mid to high frequencies at night. Whistle characteristics analysis revealed that the frequencies and range of the whistles were different to those previously reported under similar conditions. Whistles varied diurnally and in the presence of fish chorus and fishing boats. The study highlights a strong correlation between fish choruses and whistle detection. Temporal and spatial models showed that whistle detections varied monthly and in relation to fish noise and small vessel engine noise. Dolphins were distributed throughout most of the study area; however, whistle detections varied with distance from the coast. The results provide new knowledge about background noise composition in this region and provide the first information on the ecology of dolphin whistles in relation to this background noise, especially to fish chorus.

Cette thèse constitue une analyse de la dynamique du bois mort en rivière par une approche de bilan ligneux multi-scalaire dans une rivière semi-alluviale de région froide: la rivière Saint-Jean, Gaspé. L’étude de la variabilité spatiale et temporelle de la dynamique du bois mort a été réalisée grâce à une approche méthodologique combinant quatre années de terrain et par l’analyse de documents historiques. Les rivières de la péninsule gaspésienne produisent et transportent annuellement de grandes quantités de bois mort. Cette production provient à la fois de la puissance spécifique élevée des cours d’eau et de berges composées de sédiments peu cohésifs et comportant une ripisylve arborescente généralement dense. Jusqu’en 2015, le delta de la rivière Saint-Jean comportait plusieurs embâcles de bois de très grandes tailles. Ces embâcles se mettent en place depuis les années 1960, ils représentent une opportunité unique de quantifier et d’appliquer un budget ligneux pour cerner les variables clefs liées à la dynamique du bois mort à multiples échelles spatiales et temporelles.Nos résultats montrent que la quasi-totalité des bois morts en rivière est produite par la migration latérale et par l’influence de la morphologie. Au niveau des accumulations dans le corridor fluvial, deux zones accumulent la majorité des bois et ces premiers résultats montrent une mobilité importante qui peut varier fortement d'une année à l'autre. Au niveau de la mobilité, l’analyse d’imagerie vidéo de trois évènements différents ont montré que l’intensité (nombre de bois par minute) du transport de bois pouvait être jusqu’à dix fois supérieures durant un évènement avec débâcle mécanique glacielle, comparativement à un évènement hydroclimatique en eau libre.Finalement, nous avons réalisé une analyse par bilans ligneux et une analyse de la trajectoire éco-hydrophormologique sur une période de plus de 50 ans. Nous avons quantifié chaque composante (intrant, accumulée et sortie) d'un budget ligneux à multiples échelles spatio-temporelles. Autant à l’échelle interannuelle, qu’à l’échelle décennale, la dynamique du bois mort comporte des périodes où l’entrée de bois, le stockage et la mobilité diffèrent selon les contextes éco-hydromorphologiques. La trajectoire éco-hydromorphologiques suggère une augmentation de la dynamique fluviale en raison d'un changement significatif dans l'hydrologie conduisant à une plus grande production et mobilité des bois morts et par l'augmentation des volumes accumulés dans le corridor de la RSJ depuis 2004. / This thesis is an analysis of the dynamics of large wood in river by a multi-scale large wood budget approach in a semi-alluvial river of cold regions: the Saint-Jean River, Gaspé. The study of the spatial and temporal variability of the dynamics of large wood was carried out through a methodological approach combining four years of field and by analyzing historical documents. The rivers of the Gaspé Peninsula produce annually and carry large amounts of large wood. This production comes from the high specific power of rivers and by banks composed of noncohesive sediment and having a generally dense riparian forest tree. Until 2015, the Delta of the Saint-Jean River had several very large jams. These jams are put in place since the 1960s, they represent a unique opportunity to quantify and apply a wood budget and to identify key variables related to the dynamics of large wood at multiple spatial and temporal scales.Our results show that almost all large wood in river is produced by lateral migration and by the influence of the morphology. For the accumulations in the river corridor, two areas accumulate the majority of wood and these first results show a significant mobility, which can fluctuate substantially from year to year. In terms of mobility, video analysis of three different events showed that the intensity of the transport (number of large wood per minute) can be higher to ten times during an event with mechanical ice-breakup, compared to an open water.hydroclimatic event.Finally, we conducted an analysis by large wood budget and analysis of eco-hydromorphological trajectory over more than 50 years. We quantified each component (input, output and accumulated) of a large wood budget at multiple spatial and temporal scales. At the interannual scale or decadal, scale, the dynamics of large wood have periods when the input, storage and mobility of large wood differ according to eco-hydromorphological contexts. The eco-hydromorphological trajectory suggests an increase in river dynamics due to a significant change in the hydrology, resulting in higher production and mobility of large wood and increased in volumes accumulated in the corridor of the Saint-Jean River since the last decade.

The widespread adoption of photonic circuits requires the economics of volume manufacturing offered by integration technology. A Complementary Metal-Oxide Semiconductor compatible silicon material platform is particularly attractive because it leverages the huge investment that has been made in silicon electronics and its high index contrast enables tight confinement of light which decreases component footprint and energy consumption. Nevertheless, there remain challenges to the development of photonic integrated circuits. Although the density of integration is advancing steady and the integration of the principal components – waveguides, optical sources and amplifiers, modulators, and photodetectors – have all been demonstrated, the integration density is low and the device library far from complete. The integration density is low primarily because of the difficulty of confining light in structures small compared to the wavelength which measured in micrometers. The device library is incomplete because of the immaturity of hybridisation on silicon of other materials required by active devices such as III-V semiconductor alloys and ferroelectric oxides and the difficulty of controlling the coupling of light between disparate material platforms. Metamaterials are nanocomposite materials which have optical properties not readily found in Nature that are defined as much by their geometry as their constituent materials. This offers the prospect of the engineering of materials to achieve integrated components with enhanced functionality. Metamaterials are a class of photonic crystals includes subwavelength grating waveguides, which have already provided breakthroughs in component performance yet require a simpler fabrication process compatible with current minimum feature size limitations. The research reported in this PhD thesis advances our understanding of the structure-property relations of key planar light circuit components and the metamaterial engineering of these properties. The analysis and simulation of components featuring structures that are only just subwavelength is complicated and consumes large computer resources especially when a three dimensional analysis of components structured over a scale larger than the wavelength is desired. This obstructs the iterative design-simulate cycle. An abstraction is required that summarises the properties of the metamaterial pertinent to the larger scale while neglecting the microscopic detail. That abstraction is known as homogenisation. It is possible to extend homogenisation from the long-wavelength limit up to the Bragg resonance (band edge). It is found that a metamaterial waveguide is accurately modeled as a continuous medium waveguide provided proper account is taken of the emergent properties of the homogenised metamaterial. A homogenised subwavelength grating waveguide structure behaves as a strongly anisotropic and spatially dispersive material with a c-axis normal to the layers of a one dimensional multi-layer structure (Kronig-Penney) or along the axis of uniformity for a two dimensional photonic crystal in three dimensional structure. Issues with boundary effects in the near Bragg resonance subwavelength are avoided either by ensuring the averaging is over an extensive path parallel to boundary or the sharp boundary is removed by graded structures. A procedure is described that enables the local homogenised index of a graded structure to be determined. These finding are confirmed by simulations and experiments on test circuits composed of Mach-Zehnder interferometers and individual components composed of regular nanostructured waveguide segments with different lengths and widths; and graded adiabatic waveguide tapers. The test chip included Lüneburg micro-lenses, which have application to Fourier optics on a chip. The measured loss of each lens is 0.72 dB. Photonic integrated circuits featuring a network of waveguides, modulators and couplers are important to applications in RF photonics, optical communications and quantum optics. Modal phase error is one of the significant limitations to the scaling of multimode interference coupler port dimension. Multimode interference couplers rely on the Talbot effect and offer the best in-class performance. Anisotropy helps reduce the Talbot length but temporal and spatial dispersion is necessary to control the modal phase error and wavelength dependence of the Talbot length. The Talbot effect in a Kronig-Penny metamaterial is analysed. It is shown that the metamaterial may be engineered to provide a close approximation to the parabolic dispersion relation required by the Talbot effect for perfect imaging. These findings are then applied to the multimode region and access waveguide tapers of a multi-slotted waveguide multimode interference coupler with slots either in the transverse direction or longitudinal direction. A novel polarisation beam splitter exploiting the anisotropy provided by a longitudinally slotted structure is demonstrated by simulation. The thesis describes the design, verification by simulation and layout of a photonic integrated circuit containing metamaterial waveguide test structures. The test and measurement of the fabricated chip and the analysis of the data is described in detail. The experimental results show good agreement with the theory, with the expected errors due to fabrication process limitations. From the Scanning Electron Microscope images and the measurements, it is clear that at the boundary of the minimum feature size limit, the error increases but still the devices can function.

Broadband spectral content is required to support ultrashort pulses. However this broadband content is subject to dispersion and hence the pulse duration of corresponding ultrashort pulses may be stretched accordingly. I used a commercially-available adaptive ultrashort pulse shaper featuring multiphoton intrapulse interference phase scan technology to characterise and compensate for the dispersion of the optical system in situ and conducted experimental and theoretical studies in various inter-linked topics relating to the light-matter interaction. Firstly, I examined the role of broadband ultrashort pulses in novel light-matter interacting systems involving optically co-trapped particle systems in which inter-particle light scattering occurs between optically-bound particles. Secondly, I delivered dispersion-compensated broadband ultrashort pulses in a dispersive microscope system to investigate the role of pulse duration in a biological light-matter interaction involving laser-induced cell membrane permeabilisation through linear and nonlinear optical absorption. Finally, I examined some of the propagation characteristics of broadband ultrashort pulse propagation using a computer-controlled spatial light modulator. The propagation characteristics of ultrashort pulses is of paramount importance for defining the light-matter interaction in systems. The ability to control ultrashort pulse propagation by using adaptive dispersion compensation enables chirp-free ultrashort pulses to be used in experiments requiring the shortest possible pulses for a specified spectral bandwidth. Ultrashort pulsed beams may be configured to provide high peak intensities over long propagation lengths, for example, using novel beam shapes such as Bessel-type beams, which has applications in biological light-matter interactions including phototransfection based on laser-induced cell membrane permeabilisation. The need for precise positioning of the beam focus on the cell membrane becomes less strenuous by virtue of the spatial properties of the Bessel beam. Dispersion compensation can be used to control the temporal properties of ultrashort pulses thus permitting, for example, a high peak intensity to be maintained along the length of a Bessel beam, thereby reducing the pulse energy required to permeabilise the cell membrane and potentially reduce damage therein.