L’intérêt des artistes pour les biotechnologies remonte aux années 1990. De nombreux travaux universitaires se sont penchés depuis sur ces interactions entre art et biotechnologie. En regardant de plus près les œuvres conçues à l’aide des biotechnologies, on s’aperçoit de leur importance dans l’œuvre. Comment l’utilisation des nouvelles technologies révèle-t-elle une évolution de l'appréhension artistique du vivant ? Ouvrir la réflexion au vivant, c’est-à-dire êtres humains, animaux et végétaux, permet de rendre compte d’une tentative de dépasser l’anthropocentrisme, tout en soulignant la dépendance des autres vivants envers l’espèce humaine. Les œuvres sont autant de scénarios qui, s’ils ne sont pas nécessairement pertinents sur le plan scientifique, permettent d’évoquer les enjeux des avancées technologiques. L’envie de dépasser les limites humaines, les rêves d’hybridation entre humain et machine, et le refus de la mort viennent alimenter l’imaginaire artistique. A travers une sélection d'œuvres d'Art Orienté objet, de Wim Delvoye, d’Eduardo Kac, d’ORLAN, et de Stelarc, trois grandes thématiques structurent cette réflexion : la mort (et la vie), le sexe et l'hybridation. Les œuvres y sont analysées sur le plan formel, matériel, et conceptuel. Les éléments d’analyse soulignent l'importance des notions de flux, de médium, et de reproduction dans l'interaction entre art et biotechnologie. L’hybridation des connaissances, des matériaux, des pratiques, des formes, visible dans les œuvres, participe-t-elle à une nouvelle vision de l’être vivant ? / Artists's interests in biotechnologies date back from the 90's. Since then, numerous academic works focused on these interactions between art and biotechnology. By taking a closer look on works of arts conceived through the use of biotechnologies, we realize their impact in the work. How the use of new technologies demonstrates an evolution of the artistic perception of the living ? Opening the reflection on the living, understood as human beings, animals and plants, allows to take notice of an attempt to go beyond anthropomorphism while emphasizing the connection/dependency between the other living beings and the human specie. The works of art are as many scenarios which, if not necessary relevant on a scientific level, allow to think about the issues raised by technologic developments. The wish to go beyond human limits, dreams of hybridization between human and machine, and the refusal of death feed the artistic imaginary. Through as selection of works from Art Orienté objet, Wim Delvoye, Eduardo Kac, ORLAN and Stelarc, three big themes will be at the core of this reflection: death (and life), sex, and hybridization. The works will be analyzed through a formal, material and conceptual perspective. These elements allow us to emphasize the notion of flow in the interaction between art and biotechnology. Is the hybridization of knowledge, material, practices, shapes, which is visible in the aforementioned works, part of the new vision of the living being?

Understanding the strategies that plant populations implement to increase evolutionary responsiveness to better survive environmental changes induced by climate change is a critical challenge for ecology and evolutionary studies. This dissertation investigates the role of hybridization, local adaptation, and phenotypic plasticity in plant population responses to environmental change. Specifically, I utilized meta-analysis techniques to investigate the prevalence of local adaptation and phenotypic plasticity as the two main mechanisms used to adapt to heterogeneous environments, and experimentally explored the genetic pathway of plasticity in phenology traits such as bolting time in Arabidopsis thaliana under high temperatures. Furthermore, A. thaliana was used to create artificial hybrids to test if novel trait combinations allow hybrids to outperform their parental source in novel and stressful environments. In the second chapter, I included reciprocal transplant plant studies and found that local adaptation is more common than adaptive plasticity as an evolutionary response to environmental heterogeneity. Although local adaptation was more common, plastic responses have been reported as a mechanism to tolerate increases in global temperature; however, the underlying genetic and developmental mechanisms are only starting to be elucidated. To address this, the third chapter determined whether alternative splicing of the ambient temperature flowering pathway gene FLOWERING LOCUS-M (FLM), and expression of SHORT VEGETATIVE PHASE (SVP), can explain flowering time plasticity in ecotypes of A. thaliana under 18°C and 26°C. Although the expression of SVP and FLM-β tracks reaction norms, I failed to find evidence that alternative FLM splicing plays a role in phenotypic plasticity in intraspecific flowering time variation. Intraspecific hybridization (admixture) disrupts divergent genetic architectures between populations to generate phenotypic novelty and raw material for environmental selection to act upon. In order to understand the effect of this disruption to local adaptation of A. thaliana ecotypes separated along geographic and locally adaptive genetic distances, the fourth chapter used experimentally created F1-hybrids between geographically distant ecotypes, and used single nucleotide polymorphism (SNP) data to estimate (putatively neutral) background and adaptive genetic distances. My results suggest that disruption of locally adaptive genomic loci decreases the performance of offspring between distantly related parents, but that crosses between very closely related parents also reduce performance, suggesting that during admixture selection may have to balance the consequences of disrupting local adaption while also avoiding inbreeding depression. Lastly, I examined the effect of recombination events under limiting and novel growing conditions (i.e. drought, high temperatures, and freezing field over-wintering conditions) in A. thaliana F2-hybrids. I provide empirical data for the effect of limiting growing environment on phenology, growth, and fitness traits on the admixed and parental ecotypes. I found that recombination events generate novel phenotypes. Generally, offspring phenotypic variation increases and shifts from the parental ecotype phenotypes, and in some cases, offspring display transgressive segregation, heterosis, or outbreeding depression. This work provides a novel contribution towards understanding mechanisms that plant implement to deal with rapid environmental changes. Specifically, plastic responses and hybridization events may interplay to maintain and increase genotypic diversity.

Two plaque-pure phage lambda clones designated as λhtX-l and λhtX-2 that hybridized to unfractionated bovine liver tRNA were isolated from a human X chromosome-specific library. The λDNAs were characterized by restriction mapping and Southern blot hybridization techniques. The human DNA segment in λhtX-l contains five or more presumptive tRNA genes and at least one Alu family member. The 19-kilobase human DNA insert in λhtX-2 contains two or more presumptive tRNA genes and at least three Alu family members. Another human genomic clone designated λhVKV7 hybridized to mammalian valine tRNA IAC. The clone was characterized by physical mapping and Southern blot hybridization techniques. The 18.5-kilobase human DNA fragment in λhVKV7 contains a cluster of three tRNA genes and at least nine Alu family members.

Sexual reproduction entails complex co-evolution between the sexes, necessary for successful fertilization, ensuring individual and population-level fitness. Interfertility is the main criterion for species definition and understanding speciation requires detailed studies of reproductive barriers. However, many studies on reproductive barriers are constrained to infer evolutionary processes from patterns. In this thesis, I focus on a hybrid zone between collared and pied flycatchers (Ficedula albicollis and hypoleuca) on the island of Öland, and a trait that is essential for fertilization: sperm. Long-term monitoring of these species, combined with recent advances in molecular tools, allow me to study how complex on-going intersexual and interspecific interactions influence reproductive isolation in this young hybrid zone. I start by exploring the links between pre- and postmating sexual selection within collared flycatchers (paper I and II). I show that secondary sexual characters and indirect mate-choice benefits are tightly linked to physiology (paper I), and that a male’s attractiveness and dominance status dictate which sperm traits are optimal, as a male’s fertilization success depends on an interaction between sperm and display traits (paper II). I then report a source of strong postzygotic isolation between recently diverged collared and pied flycatchers: impaired spermatogenesis resulting in absence of mature sperm cells in hybrid males (paper III). I show however that pied flycatcher females, who are most exposed to hybridization, can mitigate these costs through mechanisms of cryptic female choice impairing heterospecific sperm performance, allowing them to bias paternity towards pure-species offspring (paper IV). Finally, by exploring the testes transcriptomes and sperm proteomes of both species, I highlight the importance of gene and protein regulation mechanisms in facilitating phenotypic divergence between these species (paper V). Thus, my thesis reveals complex interactions between primary and secondary sexual characters in a wild bird and suggests that mechanisms of sexual selection are tightly linked to essential physiological functions. I also show that genetic incompatibilities can evolve rapidly despite low genome-wide levels of divergence but that divergence in regulatory regions and proteins potentially allows fast evolution of molecular mechanisms impairing or preventing costly heterospecific fertilization.

Ma thèse s'inscrit dans le cadre de l'étude de l'impact des changements environnementaux sur la biodiversité marine, à une échelle intra-spécifique et inter-spécifique. Les modèles choisis sont des Octocoralliaires méditerranéens (corail rouge; Corallium rubrum, et gorgones Paramuricea clavata et Eunicella cavolini). Mieux comprendre les conséquences génétiques des fluctuations passées sur les organismes permet d'appréhender les conséquences génétiques à venir des changements environnementaux en cours. Durant ma thèse, nous avons donc étudié par une approche de phylogéographie comparée l'évolution de ces espèces : plusieurs marqueurs de séquences ont été utilisés afin de tenter de détecter des changements démographiques passés et de reconstituer l'histoire évolutive de ces espèces. L'étude du complexe d'espèces du genre Eunicella a mis en évidence que des limites d'espèces floues entre E. cavolini et E. singularis liés à de possibles flux de gènes entre elles. Par ailleurs, l'impact du changement climatique en cours a été étudié en conditions expérimentales. En aquarium, les résultats obtenus sur E. cavolini ont permis de détecter des phénomènes d'adaptation en présence de flux de gènes. En complément, l'étude de la phénologie de deux espèces, P. clavata et E. cavolini, a été initiée et suggère la possibilité de maintien de niveaux comparables d'effort reproducteur entre différents régimes thermiques. A travers diverses collaborations, cette thèse a permis à la fois de développer de nouveaux modèles mais aussi de réaliser une approche intégrative de l'étude de l'adaptation des Octocoralliaires de Méditerranée face au changement climatique passé et en cours. / My PhD thesis is in the context of the study of the impact of environmental changes on marine biodiversity, with an intra-specific and inter-specific level. Selected models are Mediterranean octocorals (red coral Corallium rubrum and gorgonians Paramuricea clavata and Eunicella cavolini). Better understanding the genetic consequences of these past fluctuations on organisms will help us understanding the potential future consequences of current climate change. During my PhD, we studied the evolution of these species through comparative phylogeography: several nuclear loci were used to try to detect past demographic changes and to reconstruct the evolutionary history of these species. The study of the Eunicella spp. species complex showed that genetic boundaries between E. cavolini and E. singularis were not clear with potential gene flow between them. Moreover, the impact of ongoing climate change has been studied in experimental conditions. In aquariums, the results obtained on E. cavolini have revealed adaptive processes in the presence of gene flow. Through various collaborations, this thesis has allowed both to develop new models but also to achieve an integrative approach of the study of the adaptation of Mediterranean octocorals facing past and ongoing climate change.

The methods presented in this study are aimed at the identification of subpopulations (clones) of genetically similar cells within tissue samples through measurement of loci-specific Fluorescence in-situ hybridization (FISH) spot signals for each nucleus and analyzing cell spatial distributions by way of Voronoi tessellation and Delaunay triangulation to robustly define cell neighbourhoods. The motivation for the system is to examine lung cancer patient for subpopulations of Non-Small Cell Lung Cancer (NSCLC) cells with biologically meaningful gene copy-number profiles: patterns of genetic alterations statistically associated with resistance to cis-platinum/vinorelbine doublet chemotherapy treatment. Current technologies for gene-copy number profiling rely on large amount of cellular material, which is not always available and suffers from limited sensitivity to only the most dominant clone in often heterogeneous samples. Thus, through the use of FISH, the detection of gene copy-numbers is possible in unprocessed tissues, allowing identification of specific tumour clones with biologically relevant patterns of genetic aberrations. The tissue-wide characterization of multiplexed loci-specific FISH signals, described herein, is achieved through a fully automated, multicolour fluorescence imaging microscope and object segmentation algorithms to identify cell nuclei and FISH spots within. Related tumour clones are identified through analysis of robustly defined cell neighbourhoods and cell-to-cell connections for regions of cells with homogenous and highly interconnected FISH spot signal characteristics. This study presents experiments which demonstrate the system’s ability to accurately quantify FISH spot signals in various tumour tissues and in up to 5 colours simultaneously or more through multiple rounds of FISH staining. Furthermore, the system’s FISH-based cell classification performance is evaluated at a sensitivity of 84% and specificity 81% and clonal identification algorithm results are determined to be comparable to clone delineation by a human-observer. Additionally, guidelines and procedures to perform anticipated, routine analysis experiments are established. / Science, Faculty of / Physics and Astronomy, Department of / Graduate

The pathogen Campylobacter fetus (CF) is classified into two subspecies, Campylobacter fetus subspecies fetus (CFF) and Campylobacter fetus subspecies venerealis (CFV). Even though CFF and CFV are genetically closely related, they exhibit differences in their host adaptation; CFF inhabits the gastrointestinal tract of both humans and several animal species, while classical CFV is specific to the bovine genital tract and is of particular concern with respect to international bovine trade regulation. Traditionally, differentiation between the two subspecies has been achieved using a limited number of biochemical tests but more rapid and definitive genetic methods of discrimination are desired. A recent study suggested that the presence of a genomic island only in CFV could discriminate between the two sub- species but this hypothesis could not be confirmed on a collection of isolates originating in Canada. To identify alternative gene targets that would support accurate subspecies discrimination, this study has applied several approaches including suppression subtractive hybridization and whole genome sequencing supplemented with optical mapping. A subtractive hybridization screen, using a well-characterized CFV isolate recovered during routine screening of bulls in an Artificial Insemination center in western Canada and that lacked much of the genomic island and a typical Canadian CFF isolate, yielded 50 clones; characterization of these clones by hybridization screening against selected CF isolates and by nucleotide sequence BLAST analysis identified three potentially CFV-specific clones that contained inserts originating from a second genomic island. Further screening using a larger CF sample set found that only Clone #35 was truly CFV-specific. Optical maps (NcoI digest) of the Canadian CFF and CFV isolates used for the subtractive hybridization showed that certain regions of these genomes were quite distinct from those of two reference strains. Whole genome sequencing of these two isolates identified two target genes (PICFV5_ORF548 and CFF_Feature #3) that appear to be selectively retained in the two subspecies. Screening of a collection of CF isolates by PCRs targeting these three loci (SSH_Clone #35, PICFV5_ORF548 and CFF_Feature #3) supported their use for subspecies discrimination. This work demonstrates the complex genomic diversity associated with these CF subtypes and the challenge posed by their discrimination using limited genetic loci.

La France entretient avec son voisin anglais, entre le milieu du XVIe siècle et le début des années 1640, deséchanges constants, tant d’un point de vue politique que culturel. Malgré les troubles religieux et les guerres qui agitentl’Europe occidentale durant cette période, en dépit également des barrières linguistiques, un grand nombre devoyageurs, de diplomates, d’intellectuels et d’écrivains n’hésitent pas à traverser les frontières. Ces passeurs quittent laFrance pour se rendre de l’autre côté de la Manche : ils y apprennent éventuellement la langue anglaise, effectuent desmissions diverses et surtout ils se font les acteurs de la relation culturelle entre les deux pays. Imprimés et traductions detextes religieux, scientifiques ou littéraires, mais aussi troupes théâtrales circulent ainsi de l’Angleterre vers la France,empruntant parfois des détours inattendus. L’étude s’attache dans un premier temps à passer en revue ces différentstypes de contacts et de transferts culturels, en particulier en ce qui concerne l’influence de la littérature anglaise sur lethéâtre français.Cette influence se manifeste par ailleurs à travers des conceptions et des pratiques hybrides du théâtre.Poétiques du mélange, du métissage et de l’hybridation formelle et générique sont caractéristiques du théâtre anglais dela période élisabéthaine et jacobéenne. Des auteurs comme Marlowe, Greene, Shakespeare ou Webster expérimentent eneffet des formules dramatiques qui invitent à reconsidérer et relativiser les catégories poétiques traditionnelles. Si latragédie, la comédie ou la tragi-comédie ne sont pas absentes en tant que dénominations génériques, elles sont lessupports et les instruments de combinaisons et de mélanges multiples et variés. Ce faisant, les différentes modalités dumélange et de l’hybridation dans le théâtre anglais permettent de jeter un regard différent sur la production dramatiqueen France entre la fin du XVIe siècle et le début du XVIIe siècle. En effet, les pièces composées pendant cette périodelongtemps méconnue du théâtre français, attestent d’une hybridité aussi marquée que celle des pièces anglaises, et ellestémoignent de la grande diversité des formes et des genres dramatiques. Ce théâtre, qui ne se conforme pas encore auxcatégories critiques et aux principes dramatiques formulés par les théoriciens et commentateurs d’Aristote, secaractérise par son irrégularité, la porosité de ses catégories génériques et par un souci de s’adapter aux contraintes de lavie théâtrale.L’étude s’attache dans un dernier temps à poser les prémisses d’une analyse plus approfondie des liensorganiques entre le théâtre médiéval et populaire et le théâtre français à l’aube du XVIIe siècle. Ainsi, ce que nousappelons « théâtre monstre », parce qu’il a partie liée avec la figure politique, symbolique et esthétique du monstre etses différentes déclinaisons, nous permet de rapprocher, en France et en Angleterre, des pièces qui se caractérisent parleur a-normalité, leur ludisme et leur métathéâtralité, loin de la tradition aristotélicienne et de ses contraintes. Noussommes amené ainsi à considérer le théâtre français selon sa diversité géographique et linguistique, ainsi que du pointde vue de ses continuités historiques. / France maintains with its English neighbor, between the mid-sixteenth century and the early 1640’s, constantrelationships, both political and cultural. Despite the religious troubles and the wars shaking the western Europe duringthis period, despite linguistic barriers, many travelers, diplomats, intellectuals and writers cross the frontiers. Thesecultural travelers leave France to go abroad, to the other side of the Channel : they eventually learn the Englishlanguage, carry out various missions and, above all, they become the actors of the cultural relationship between the twocountries.This influence is also evident through conceptions and hybrid practices of theater. Poetics of mixing, of formaland generic hybridizations are characteristic of the English theater during the Elizabethan and Jacobean period. Authorslike Marlowe, Greene, Shakespeare and Webster experiment new dramatic formulas that invite us to reconsider andrelativize the traditional poetic categories. Tragedy, comedy or tragicomedy are not absent as generic designations, butthey are the medias and instruments of combinations, and of multiple and various blends. Thus, the different ways ofmixing and mingling in the English theater make possible a different look at the dramatic production in France duringthe late XVIth and early 17th century. Indeed, the plays written during this long unrecognized period of the Frenchtheater, show a hybridity as marked as in the English plays and they reflect the great diversity of forms and dramaticgenres. This theater, which does not conform to the critical categories and dramatic principles formulated by theoristsand commentators of Aristotle, is characterized by its irregularity, the porosity of its generic categories and by a desireto adapt to the constraints of the theatrical life.Finally, the study focuses on the premises of a more thorough analysis of organic links between the medievaland popular theater and the French theater at the dawn of the 17th century. Thus, what we call « monster theater »,because of its bounds with the political, symbolic and aesthetic figure of the monster and its various configurations,allows us to compare, in France and England, plays that are characterized by their ab-normality, their playful dimensionand their metatheatrality, far away from the Aristotelian tradition and its constraints. In this way, we are led to considerthe French theater according to its geographical and linguistic diversity, but also from the perspective of its historicalcontinuities.

The role of divergent climate adaptation in speciation has received surprisingly little scientific attention. My dissertation research focused on how resting metabolic rate (RMR) relates to the build up of prezygotic and postzygotic isolation in a natural Ficedula flycatcher hybrid zone. RMR is the amount of energy an organism needs to run its internal organs. Since RMR is related to life history traits and thermoregulation in other systems, it is likely to affect speciation processes at secondary contact. I found that adult collared flycatchers displace pied flycatchers into increasingly poor habitats (Paper I). Pied nestlings exhibit lower RMR in poor environments (Paper II), which may promote regional coexistence and habitat isolation by making it possible for pied flycatchers to escape competition from collared flycatchers and reduce the risk of hybridization by breeding in the poorer habitats. Further, I found that while collared flycatcher nestling RMR was not environmentally-dependent (Paper II, Paper III), those collared flycatcher nestlings that had a lower RMR in poor environments tended to have higher condition (Paper III). Further, RMR was genetically linked to a sexual ornament in collared males that has previously been shown to be beneficial in poor environments. Lastly, I found that by seven days old, nestlings increase their metabolic rate when listening to song, indicating that they are listening, and by 9 days they can discriminate between songs (Paper IV). Taken together, RMR could affect pre-zygotic isolation via correlations with life history strategies, song and sexual ornaments. RMR is also related to post zygotic isolation in Ficedula flycatchers. I found that flycatcher hybrids tended to have a higher RMR than the parental species (Paper V), and that there were many differentially expressed genes in energetically expensive organs in hybrids that were related to metabolic function (Paper VI). Thus, metabolic dysfunction, possibly caused by genetic incompatibilities, in Ficedula flycatcher hybrids could be a factor leading to infertility and postzygotic isolation between the parental species. Overall, I find that RMR could be a general physiological trait that affects both pre- and postzygotic isolation in hybridizing species at secondary contact, and ought to be more thoroughly considered in speciation research.

As gramíneas do gênero Paspalum são as principais constituintes das pastagens nativas em vários países das Américas, fornecendo excelente forragem nas pastagens naturais destas regiões. Além disso, possuem grande potencial para exploração em programas de melhoramento genético visando o estabelecimento de pastagens cultivadas. No entanto, a apomixia é o modo de reprodução predominante nas espécies poliplóides de Paspalum, o que dificulta a recombinação gênica. Assim, o emprego de hibridações, quando um dos genitores apresenta reprodução sexuada, pode gerar variabilidade e possibilitar a seleção de progênies elite, com a fixação dos caracteres de interesse através da apomixia. A descoberta de plantas diplóides sexuais de Paspalum plicatulum e sua indução à tetraploidia obtida a partir destes, tornaram possível cruzamentos interespecíficos entre várias espécies do grupo Plicatula a nível tetraplóide. O objetivo deste estudo foi avaliar a magnitude de expressão de caracteres de interesse forrageiro de híbridos interespecíficos (P. plicatulum x P. guenoarum) obtidos por meio de cruzamentos entre espécies do grupo Plicatula em diferentes ambientes e anos de avaliação. Os resultados indicaram que as variáveis massa seca total e massa seca de folhas apresentam maior magnitude na identificação dos genótipos com características agronômicas desejáveis recebendo grande influência da interação genótipo e ano de cultivo. A seleção a partir do segundo ano em híbridos interespecíficos de Paspalum é a mais indicada, considerando a expressão do seu potencial produtivo. A produção de massa seca total é o caráter que mais se correlaciona com a produção de massa seca de folhas em genótipos de Paspalum. Os híbridos que apresentam caracteres agronômicos superiores, principalmente para a produção de forragem e tolerância ao frio, demonstram potencial para serem lançados como cultivares, pois já possuem os caracteres desejados fixados pela apomixia. Além disso, podem ser utilizados em novos cruzamentos com plantas sexuais superiores dentro do programa de melhoramento, visando a obtenção de novos recombinantes elites. / The grasses of the genus Paspalum are the main constituents of the native pastures in several countries of the Americas, providing excellent forage on these regions. Furthermore, they have great potential for exploitation in breeding programs for the establishment of cultivated pastures. However, apomixis is the predominant mode of reproduction in polyploid species of Paspalum, which hampers genetic recombination. Thus, the use of hybridizations, when one parent has sexual reproduction, may generate variability and enable the selection of elite progenies, with characteristics of interest fixed by apomixis. The discovery of sexual diploid Paspalum plicatulum and its induction of tetraploidy, madepossible interspecific crosses between various species of the group Plicatula at the tetraploid level. The objective of this study was to evaluate the magnitude of expression of characters of forage interest of interspecific hybrids (P. plicatulum x P. guenoarum) obtained by crosses between species of the Plicatula group in different environments and years of evaluation. The results indicated that total dry mass and dry mass of leaves variables showed variability in identifying genotypes with desirable agronomic characteristics, received significant influence of genotype and year of cultivation. A selection from the second year in interspecific hybrids of Paspalum is more appropriate, considering the expression of their productive potential. The total dry mass is the character that most closely correlates with the production of dry mass of leaves in genotypes of Paspalum. The hybrids showing superior agronomic traits, primarily for forage production and cold tolerance, demonstrate potential to be released as cultivars, since they already have the desired characters fixed by apomixis. Besides, could also be used for new crosses with superior sexual plants within the breeding program aiming to obtain new elite recombinant.