During fin regeneration, a blastema, a group of de-differentiated cells, forms underneath the wound epidermis. As regeneration proceeds, cells leave the proximal blastema and enter the differentiation zone. Adjacent to the differentiation zone, a subset of cells in the basal epidermal layer (BEL) express sonic hedgehog a (shha). Cells that come in contact with BEL differentiate into osteoblasts and joint cells, enabling the formation of bone segments at the end of each fin ray. Generally, fin regeneration occurs similarly in males and females. However, breeding tubercles (BT), keratinized epidermal structures on the male pectoral fin, result in regenerative differences when compared to females. In this thesis, three aspects of zebrafish fin regeneration were studied: 1) Cell lineage tracing of shha-expressing cells in the caudal fin regenerate; 2) The differentiation of joint cells and osteoblasts in the caudal fin regenerate; 3) Regeneration of pectoral fin BTs. Studies on caudal fin regenerates suggest osteoblasts and joint cells originate from a common cell lineage, but are committed to different cell fates. Joint cells follow a genetic pathway in which evx1 occurs downstream or parallel to hoxa13a and upstream of pthrp1. In the absence of Evx1, presumptive joint cells are committed to an osteoblast cell fate. Furthermore, joint cells do not regenerate following laser cell ablation, suggesting joint cell differentiation occurs only at specific intervals during osteoblast regeneration. Collectively, these results suggest a mechanism for joint cell differentiation during caudal fin regeneration. Studies on pectoral fins indicate androgens induce and estrogens inhibit BT formation. BT regeneration in males and androgen-treated females follows the initiation of revascularization, but occurs concomitantly with a novel second wave of angiogenesis. The inhibition of angiogenesis in androgen-treated females prevents BT formation. Altogether, these results suggest the growth and regeneration of BTs requires a v hormonal stimulus and the presence of an additional blood vessel network naturally found in males. In conclusion, these studies have increased the overall knowledge of key aspects of zebrafish fin regeneration. A gain in understanding zebrafish regeneration provides a basis in which treatments can be developed to induce regeneration in species with limited regenerative capabilities.

Traditionally, underwater vehicles have been using propellers for locomotion but they are not only inefficient but generate large acoustic signature. Researchers have taken inspiration from efficient swimmers like fish to address the issue with alternate propulsion mechanism. Mostly, research on fish locomotion involved studying a foil tethered to a fixed point inside uniform flow. A major drawback of such study is that neither it resembles a freely swimming fish nor it takes into consideration the dynamics of moving fish on propulsive forces. Hence, in our current study, we focus on comparing the performance of a free swimming fin over tethered fin both experimentally and numerically. Experimentally, we focus on the oscillatory form of locomotion where the caudal fin pitches to generate necessary thrust as seen in boxfish. We intend to investigate the Caudal fin kinematics and its physical properties on locomotion performance. To better understand, we build an automated robo-physical model that swims in a circular path so as to carry extensive experiments. We focus on understanding the effect of flexibility, shape and thickness of caudal fin on performance. Currently, we have studied three different flexibility and for each flexibility, we studied three different shape. We found there must be an optimal flexibility for minimising the Cost of Transport (COT). We also propose that the steady forward speed linearly varies with tail tip velocity. Furthermore, we investigated the effect of thickness of fin and considered uniform and tapered fin with equal area moment of inertia. Numerically, we investigated the effect of phase offset between heave and pitch motion on the performance of a freely swimming fin and compared that to a tethered fin. A freely-swimming fin self propels and moves with steady speed while a tethered fin remains stationary and actuates under uniform flow. We model the fin as a rigid body undergoing prescribed motion in an inviscid fluid and solved for coupled interaction using panel method. We show the effect of phase offset for optimum performance and found a significant difference between tethered and freely swimming fin. / M.S. / Underwater vehicles use propeller based mechanism but they are inefficient and generate noise. Researchers have taken inspiration from nature to replace propellers with efficient propulsion mechanism. In the current study, we design a robotic model to understand the effect of various kinematic and physical properties of tail fin on performance. Our research is unique from past study in the aspect that most research involved studying performance using a robotic model fixed at its position which does not resemble a freely-swimming fish. Hence, in our current study, we focus on comparing the performance of our freely swimming model with tethered fin. The robot has one degree of freedom and can pitch its tail to generate thrust. We intend to investigate the tail fin kinematics and its physical properties on locomotion performance. We focus on understanding the effect of flexibility, shape and thickness of fin on performance. Currently, we have studied three different flexibility and for each flexibility, we studied three different shape. We showed there exists an optimal flexibility for maximising efficiency. For any fin undergoing combined pitch and heave motion, there exists a phase offset between them which will maximise the performance. Researchers have tried to understand its impact using both experiment and numerical simulation. In the current study, we study the impact of phase offset between pitch and heave for a freely-swimming fin and compare that to a fixed fin. A freely-swimming fin self propels and moves with steady speed while a tethered fin remains stationary and actuates under uniform flow. We show the effect of phase offset for optimum performance and found a significant difference between tethered and freely swimming fin.

The versatility of the fish to adapt to diverse swimming requirements has attracted the attention of researchers in studying bioinspired propulsion for developing efficient underwater robotics. The tail/caudal fin is a major source of thrust generation and is believed that the fish modulates its fin stiffness to optimize the propulsive performance. Inspired by the stiffness modulation of fish fins, the objective of this research is to predict and evaluate the effect of flexibility on propulsive performance of flapping fins. The stiffness of the fins vary along their length and optimization studies have been performed to predict the stiffness profiles that maximize performance. Experiments performed on the real fish caudal fins to measure the stiffness variation along their length validate the theoretical optimal stiffness profiles and provide an insight about the evolution of fish fins for optimal performance. Along with the fin stiffness, the stiffness of the joint (caudal peduncle) connecting the fish body to the tail plays a major role in the generation of thrust. The numerical and experimental investigation has shown that there exists an optimal combination of fin and joint stiffness for each operating condition, thus providing the motivation for active stiffness control during locomotion to optimize efficiency. Inspired by nature's ability to modulate stiffness and shape for different operating conditions, an investigation has been carried out on active control of flapping foils for thrust tailoring using Macro Fiber Composites (MFCs). It has been observed that the performance can be enhanced by controlling the deformation, and distributed actuation along fin produces maximum performance through proper selection of the phase difference between heaving and voltage. Flapping fins produce forces which are oscillatory in nature causing center of mass (COM) oscillations of the attached bodies posing problems of control and maneuverability. Optimization studies have revealed that flexibility of the fin plays a major role in reducing the COM oscillations along with the other operating parameters. Based on these studies, the design principles and guidelines that control the performance have been proposed which aid in the development of aerial and underwater robotic vehicles. Additionally, these studies provide some insight in to how fish might modulate its stiffness based on the requirements. / Ph. D.

L'acide rétinoïque (AR) est un morphogène dérivé de la vitamine A, qui intervient dans le contrôle de l'organogenèse, de la prolifération et de la différenciation cellulaires chez les Chordés. Dans ce contexte, nous avons étudié les régulations spatio-temporelles de la voie de signalisation de l’AR au cours du développement de l’amphioxus, en mettant l'accent sur l’espèce européenne Branchiostoma lanceolatum.Nous avons tout d'abord inhibé ou activé la voie de signalisation de l’AR lors du développement embryonnaire en traitant des embryons d’amphioxus à des doses variables de composés pharmacologiques interférant avec le métabolisme des rétinoïdes. Grâce à l’utilisation d’outils mathématiques spécifiques, nous avons établi un schéma détaillé des effets des traitements effectués sur le développement du système nerveux central (SNC) et du pharynx chez l’amphioxus en nous basant sur l’expression de gènes marqueurs de tissus spécifiques. À l’issue de cette première analyse, nous avons par la suite étudié les effets d’une perturbation de la signalisation de l’AR à des points clés du développement chez l’amphioxus lors de la régionalisation du SNC et du pharynx. Nous avons ainsi montré que la voie de signalisation de l’AR intervient dans la régionalisation de l’axe antéro-postérieur via le contrôle des gènes hox dès le stade gastrula et jusqu’aux stades larvaires. En outre, nous avons réalisé l'étude préliminaire du gène homologue chez l’amphioxus du gène aldh1a2 des Vertébrés, et avons démontré que la régulation du niveau de synthèse de l’AR au cour du développement est conservée entre l’amphioxus et les Vertébrés. Finalement, nous avons montré que la voie de l’AR participe également à la morphogenèse caudale chez l’amphioxus, et que le mécanisme impliqué semble différent de celui proposé chez les Vertébrés où l’AR contrôle la structuration de la nageoire caudale par le ciblage des tissus mésenchymateux. / Retinoic acid (RA) is an endogenous vitamin A-derived morphogen. In this context, we studied the spatiotemporal roles of RA signaling in amphioxus development, focusing on the European amphioxus species: Branchiostoma lanceolatum. We first created excess and insufficiency models of RA signaling by exposing amphioxus embryos to series of doses of different pharmacological compounds targeting either the RA receptors or the RA metabolism machinery. By introducing the important mathematical concept of a Cartesian coordinate system founded by René Descartes, we created detailed diagrams of the concentration-dependent defects caused by RA signaling in the central nervous system (CNS) and pharynx of amphioxus by evaluating the statistical significances of tissue-specific marker gene expression in labeled embryos. This analysis yielded a very detailed description of the sensitivities of the developing amphioxus CNS and pharynx to altered RA signaling levels. Following this initial challenge, we correlated the effects of altered RA signaling levels with key amphioxus developmental stages characterized by structural transitions in CNS and pharynx. We show that hox-mediated RA signaling in axial patterning is active beyond the gastrula stage and might be maintained until at least early larval stage, with possible roles in more regionalized axis formation and organ induction. In addition, we carried out a preliminary study on a RA synthesizing gene in amphioxus, called aldh1a, a possible homolog of the vertebrate aldh1a2 gene, demonstrating that the feedback between RA signaling and RA synthesizing levels has emerged before the split of the cephalochordate and vertebrate lineages. Moreover, we are able to show that RA signaling also participates in tail fin morphogenesis in amphioxus by a mechanism that is probably not comparable to that in vertebrates, where RA modulates caudal fin patterning through targeting mesenchymal derivatives.