Analyzing peptides and proteins by mass spectrometry: principles and applications in proteomics

The study of proteins has been a key element in biomedicine and biotechnology because of their important role in cell functions or enzymatic activity. Cells are the basic unit of living organisms, which are governed by a vast range of chemical reactions. These chemical reactions must be highly regulatedin order to achieve homeostasis. Proteins are polymeric molecules that havetaken on the evolutionary process the role, along with other factors, of controlthese chemical reactions. Learning how proteins interact and control their up anddown regulations can teach us how living cells regulate their functions, as well asthe cause of certain anomalies that occur in different diseases where proteins areinvolved. Mass spectrometry (MS) is an analytical widely used technique to studythe protein content inside the cells as a biomarker point, which describesdysfunctions in diseases and increases knowledge of how proteins are working.All the methodologies involved in these descriptions are integrated in the fieldcalled Proteomics.

Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

Dynamic models of energy allocation and investment

In dynamic models of energy allocation, assimilated energy is allocated to reproduction, somatic growth, maintenance or storage, and the allocation pattern can change with age. The expected evolutionary outcome is an optimal allocation pattern, but this depends on the environment experienced during the evolutionary process and on the fitness costs and benefits incurred by allocating resources in different ways. Here we review existing treatments which encompass some of the possibilities as regards constant or variable environments and their predictability or unpredictability, and the ways in which production rates and mortality rates depend on body size and composition and age and on the pattern of energy allocation. The optimal policy is to allocate resources where selection pressures are highest, and simultaneous allocation to several body subsystems and reproduction can be optimal if these pressures are equal. This may explain balanced growth commonly observed during ontogeny. Growth ceases at maturity in many models; factors favouring growth after maturity include non-linear trade-offs, variable season length, and production and mortality rates both increasing (or decreasing) functions of body size. We cannot yet say whether these are sufficient to account for the many known cases of growth after maturity and not all reasonable models have yet been explored. Factors favouring storage are also reviewed.

La spéciation écologique racontée au travers de l'étude de l'évolution des poissons-clowns et de quelques autres

Ecological speciation and its hallmark, adaptive radiation is a process from which most of the current biodiversity derives. As ecological opportunity allows species to colonise unoccupied niches, natural selection drives adaptive phenotypical change. In this thesis, I begin by describing how this evolutionary process acted on the evolution of the clownfishes. During its infancy, this iconic group of coral reef fishes developed a mutualism with sea anemone species. I show how this event triggered the evolutionary radiation of the group, generating species that now inhabit diverse habitats of the coral reefs. Following the appearance of the mutualism, the diversification of the clownfish was catalysed by hybridisation events which shuffled genes, allowing hybrids to reach new fitness optima. While the clownfishes appeared in the region of the coral triangle, a lineage colonised the eastern shores of Africa. I reconstructed the geographic history of the group and showed that this event lead to the rapid appearance of new species, replicating the evolutionary patterns of the original radiation. To better grasp the mechanisms of ecological speciation, I conducted analyses at the population level and identified similar evolutionary patterns than found at the clade level. I discuss how such result suggests a continuity bridging micro- and macroevolution, which so far only been theorised. In parallel to this study case, I question whether biotic and abiotic interactions can promote or restrain ecological speciation. Indeed, I show how the ecological setting of species can drastically impact on their diversification dynamics. Moreover, tradeoffs can occur between specialisation made on different ecological axes allowing species cohabitation. Overall, I show in this work that regardless of the few simple rules that explain the mechanism of ecological speciation, the unavoidable interactions with the ever changing ecological context lead diversification events to give always a different outcome. It is thus primordial to account for the ecological settings of species when discussing their evolutionary dynamics. LA SPÉCIATION ÉCOLOGIQUE RACONTÉE AU TRAVERS DE L'ÉTUDE DE L'ÉVOLUTION DES POISSONS-CLOWNS ET DE QUELQUES AUTRES Le phénomène de spéciation écologique est à l'origine de la majeure partie de la biodiversité que l'on rencontre aujourd'hui. Au fil des opportunités qu'elles rencontrent, les espèces colonisent l'espace écologique laissant la sélection naturelle forger leur phénotype moyen. Malgré l'omniprésence de ce phénomène dans la nature, beaucoup de questions qui lui sont relatives restent à élucider. C'est afin de mieux comprendre ce mécanisme que j'étudie les poissons-clowns, célèbres habitants des récifs coralliens. Dans ce travail, je démontré que le développement du comportement mutualiste liant les poissons-clowns aux anémones de mer fut l'événement qui déclencha leur diversification. Suite à ce premier événement, j'illustre comment l'hybridation entre lignées primordiales a remodelé la diversité génétique du groupe et catalysé leur radiation évolutive. Je poursuis en reconstruisant l'expansion géographique des poissons-clowns au cours du temps depuis le triangle de corail, leur lieu d'origine, jusqu'aux côtes d'Afrique de l'Ouest. Afin d'affiner ces analyses générales sur le groupe, je continue en étudiant plus finement des populations d'une seule espèce de poisson-clown. Cette fine résolution me permet de comprendre plus précisément quels sont les facteurs écologiques qui permettent aux poissons-clowns de se différencier. Les résultats de ces analyses suggèrent qu'il est important de comprendre les liens entre le contexte écologique et la diversification des espèces. J'étudie cette question dans la seconde partie de ce travail en montrant que l'hétérogénéité du paysage ou les liens entretenus avec un partenaire mutualiste influencent fortement la dynamique évolutive des espèces. Finalement, j'illustre les compromis que chaque espèce réalise en se spécialisant ou non dans ses interactions avec l'environnent. Plus généralement, je souligne dans ce travail l'influence du contexte écologique sur le résultat de la spéciation écologique. Ce sont ces interactions entre les organismes et leur environnent qui sont à l'origine de l'incroyable diversité de la vie. Il est donc primordial de les prendre en compte lors de l'étude de l'évolution des espèces.

Artificial evolution on network structures : how time and space influence dynamics

Abstract The main objective of this work is to show how the choice of the temporal dimension and of the spatial structure of the population influences an artificial evolutionary process. In the field of Artificial Evolution we can observe a common trend in synchronously evolv¬ing panmictic populations, i.e., populations in which any individual can be recombined with any other individual. Already in the '90s, the works of Spiessens and Manderick, Sarma and De Jong, and Gorges-Schleuter have pointed out that, if a population is struc¬tured according to a mono- or bi-dimensional regular lattice, the evolutionary process shows a different dynamic with respect to the panmictic case. In particular, Sarma and De Jong have studied the selection pressure (i.e., the diffusion of a best individual when the only selection operator is active) induced by a regular bi-dimensional structure of the population, proposing a logistic modeling of the selection pressure curves. This model supposes that the diffusion of a best individual in a population follows an exponential law. We show that such a model is inadequate to describe the process, since the growth speed must be quadratic or sub-quadratic in the case of a bi-dimensional regular lattice. New linear and sub-quadratic models are proposed for modeling the selection pressure curves in, respectively, mono- and bi-dimensional regu¬lar structures. These models are extended to describe the process when asynchronous evolutions are employed. Different dynamics of the populations imply different search strategies of the resulting algorithm, when the evolutionary process is used to solve optimisation problems. A benchmark of both discrete and continuous test problems is used to study the search characteristics of the different topologies and updates of the populations. In the last decade, the pioneering studies of Watts and Strogatz have shown that most real networks, both in the biological and sociological worlds as well as in man-made structures, have mathematical properties that set them apart from regular and random structures. In particular, they introduced the concepts of small-world graphs, and they showed that this new family of structures has interesting computing capabilities. Populations structured according to these new topologies are proposed, and their evolutionary dynamics are studied and modeled. We also propose asynchronous evolutions for these structures, and the resulting evolutionary behaviors are investigated. Many man-made networks have grown, and are still growing incrementally, and explanations have been proposed for their actual shape, such as Albert and Barabasi's preferential attachment growth rule. However, many actual networks seem to have undergone some kind of Darwinian variation and selection. Thus, how these networks might have come to be selected is an interesting yet unanswered question. In the last part of this work, we show how a simple evolutionary algorithm can enable the emrgence o these kinds of structures for two prototypical problems of the automata networks world, the majority classification and the synchronisation problems. Synopsis L'objectif principal de ce travail est de montrer l'influence du choix de la dimension temporelle et de la structure spatiale d'une population sur un processus évolutionnaire artificiel. Dans le domaine de l'Evolution Artificielle on peut observer une tendence à évoluer d'une façon synchrone des populations panmictiques, où chaque individu peut être récombiné avec tout autre individu dans la population. Déjà dans les année '90, Spiessens et Manderick, Sarma et De Jong, et Gorges-Schleuter ont observé que, si une population possède une structure régulière mono- ou bi-dimensionnelle, le processus évolutionnaire montre une dynamique différente de celle d'une population panmictique. En particulier, Sarma et De Jong ont étudié la pression de sélection (c-à-d la diffusion d'un individu optimal quand seul l'opérateur de sélection est actif) induite par une structure régulière bi-dimensionnelle de la population, proposant une modélisation logistique des courbes de pression de sélection. Ce modèle suppose que la diffusion d'un individu optimal suit une loi exponentielle. On montre que ce modèle est inadéquat pour décrire ce phénomène, étant donné que la vitesse de croissance doit obéir à une loi quadratique ou sous-quadratique dans le cas d'une structure régulière bi-dimensionnelle. De nouveaux modèles linéaires et sous-quadratique sont proposés pour des structures mono- et bi-dimensionnelles. Ces modèles sont étendus pour décrire des processus évolutionnaires asynchrones. Différentes dynamiques de la population impliquent strategies différentes de recherche de l'algorithme résultant lorsque le processus évolutionnaire est utilisé pour résoudre des problèmes d'optimisation. Un ensemble de problèmes discrets et continus est utilisé pour étudier les charactéristiques de recherche des différentes topologies et mises à jour des populations. Ces dernières années, les études de Watts et Strogatz ont montré que beaucoup de réseaux, aussi bien dans les mondes biologiques et sociologiques que dans les structures produites par l'homme, ont des propriétés mathématiques qui les séparent à la fois des structures régulières et des structures aléatoires. En particulier, ils ont introduit la notion de graphe sm,all-world et ont montré que cette nouvelle famille de structures possède des intéressantes propriétés dynamiques. Des populations ayant ces nouvelles topologies sont proposés, et leurs dynamiques évolutionnaires sont étudiées et modélisées. Pour des populations ayant ces structures, des méthodes d'évolution asynchrone sont proposées, et la dynamique résultante est étudiée. Beaucoup de réseaux produits par l'homme se sont formés d'une façon incrémentale, et des explications pour leur forme actuelle ont été proposées, comme le preferential attachment de Albert et Barabàsi. Toutefois, beaucoup de réseaux existants doivent être le produit d'un processus de variation et sélection darwiniennes. Ainsi, la façon dont ces structures ont pu être sélectionnées est une question intéressante restée sans réponse. Dans la dernière partie de ce travail, on montre comment un simple processus évolutif artificiel permet à ce type de topologies d'émerger dans le cas de deux problèmes prototypiques des réseaux d'automates, les tâches de densité et de synchronisation.

Cross-border post-acquisition integration performed by a Nordic information & telecommunication technology company in the transition economy context of the Czech Republic

Diplomityön tarkoituksena oli arvioida akvisition jälkeistä integraatioprosessia. Integraation tarkoitus on mukauttaa ostettu yritys toimivaksi osaksi konsernia. Työn empiirisenä ongelmana oli yleisesti tunnustettu integraatiojohtamisen kompleksisuus. Samoin myöskin akateemisesta kirjallisuudesta puuttui koherentti malli, jolla arvioida integraatiota. Tutkimuskohteena oli akvisitio, jossa suomalainen tietotekniikkan suuryritys osti osake-enemmistön tsekkiläisestä keskisuuresta ohjelmistoyrityksestä. Tutkimuksessa generoitiin integraatiojohtamisen malli tietopohjaiseen organisaatioon. Mallin mukaan integraatio koostuu kolmesta eriävästä, mutta toisiaan tukevasta alueesta: organisaatiokulttuurin yhdentyminen, tietopääoman tasaaminen ja konsernin sisäisten prosessien yhdenmukaistaminen. Näistä kaksi kaksi jälkimmäistä ovat johdettavissa, mutta kulttuurin yhdentymiseen integraatiojohtamisella voidaan vaikuttaa vain katalysoivasti. Organisaatiokulttuuri levittäytyy vain osallisten vuorovaikuksien kautta. Lisäksi tutkimus osoitti, miten akvisitio on revolutionaarinen vaihe yrityksen kehityksessä. Integraation ensimmäinen ajanjakso on revolutionaarista. Tällöin suurimmat ja näkyvimmät johdettavat muutokset pyritään saamaan aikaan, jotta integraatiossa edettäisiin evolutionaariseen kehitykseen. Revolutionaarisen intergaation vetojuhtana toimii integraatiojohto, kun taas evolutionaarinen integraatio etenee osallisten (organisaation jäsenten) itsensä toiminnan ja vuorovaikutusten kautta.

Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, Glyphorynchus spirurus, a Neotropical rainforest bird.

Determining the relative roles of vicariance and selection in restricting gene flow between populations is of central importance to the evolutionary process of population divergence and speciation. Here we use molecular and morphological data to contrast the effect of isolation (by mountains and geographical distance) with that of ecological factors (altitudinal gradients) in promoting differentiation in the wedge-billed woodcreeper, Glyphorynchus spirurus, a tropical forest bird, in Ecuador. Tarsus length and beak size increased relative to body size with altitude on both sides of the Andes, and were correlated with the amount of moss on tree trunks, suggesting the role of selection in driving adaptive divergence. In contrast, molecular data revealed a considerable degree of admixture along these altitudinal gradients, suggesting that adaptive divergence in morphological traits has occurred in the presence of gene flow. As suggested by mitochondrial DNA sequence data, the Andes act as a barrier to gene flow between ancient subspecific lineages. Genome-wide amplified fragment length polymorphism markers reflected more recent patterns of gene flow and revealed fine-scale patterns of population differentiation that were not detectable with mitochondrial DNA, including the differentiation of isolated coastal populations west of the Andes. Our results support the predominant role of geographical isolation in driving genetic differentiation in G. spirurus, yet suggest the role of selection in driving parallel morphological divergence along ecological gradients.

Interactions of decision mechanisms in an entrepreneurial firm’s journey to become a major player in its industry

This study discusses the interactions of different decision-making mechanisms in the process of change of a successful entrepreneurial dairy firm in Vietnam. The purpose of the study is to construct a theoretical framework, which explains the interactions between effectual and causal decision-making processes in different phases of business, and to provide a real life example with practical recommendations for entrepreneurs and managers. In order to achieve this purpose, a preliminary theoretical framework was built, using process theories applied to different decision making modes, referred to as causation and effectuation. The case was studied through ethnographic research method, with three semi-structured interviews, one unstructured interview, secondary data and observations within four months in 2013-2014. After the data was analyzed, a modified framework was drawn from the result. The finding of this study shows that there was an interaction between effectual and causal decision-making processes in different stages of the company’s development. The entrepreneur applied effectual decision-making process to develop a unique business model and a new dairy market segment. However, when a new market demand arose, the company’s resources became insufficient, they thus had to shift to causation process to adapt to market change. Simultaneously, with better-accumulated resources, the entrepreneur continued the effectuation process to create another brand new dairy market segment. This study, thus, contributes to effectuation theory, emphasizing the necessity of combining effectual and causal decision-making processes in different phases of business. It is suggested that business would develop with an effectual process until a business model is viable for growth. It continues to use this process up to a certain degree. When the market changes, the company needs to collect more means to adapt to the changes. They need to set new goals and this is a shift to the use of causal process, which builds on prediction. It uses goals and teleology as driving mechanisms and tries to exploit and fill potential resource gaps to achieve these goals. At the same time, there are new iterations that look to establish new lines or types of business with the given means, which are now well established. This again employs effectual mechanisms, which are based on evolutionary process, until they reach the stage of viable tested business model. Moreover, this study hopes to provide know-how to entrepreneurs and managers of small companies in similar situations, suggesting how to combine effectual and causal decision-making processes to deal with various circumstances in different times.

Feature Selection and Classification Using Age Layered Population Structure Genetic Programming

The curse of dimensionality is a major problem in the fields of machine learning, data mining and knowledge discovery. Exhaustive search for the most optimal subset of relevant features from a high dimensional dataset is NP hard. Sub–optimal population based stochastic algorithms such as GP and GA are good choices for searching through large search spaces, and are usually more feasible than exhaustive and deterministic search algorithms. On the other hand, population based stochastic algorithms often suffer from premature convergence on mediocre sub–optimal solutions. The Age Layered Population Structure (ALPS) is a novel metaheuristic for overcoming the problem of premature convergence in evolutionary algorithms, and for improving search in the fitness landscape. The ALPS paradigm uses an age–measure to control breeding and competition between individuals in the population. This thesis uses a modification of the ALPS GP strategy called Feature Selection ALPS (FSALPS) for feature subset selection and classification of varied supervised learning tasks. FSALPS uses a novel frequency count system to rank features in the GP population based on evolved feature frequencies. The ranked features are translated into probabilities, which are used to control evolutionary processes such as terminal–symbol selection for the construction of GP trees/sub-trees. The FSALPS metaheuristic continuously refines the feature subset selection process whiles simultaneously evolving efficient classifiers through a non–converging evolutionary process that favors selection of features with high discrimination of class labels. We investigated and compared the performance of canonical GP, ALPS and FSALPS on high–dimensional benchmark classification datasets, including a hyperspectral image. Using Tukey’s HSD ANOVA test at a 95% confidence interval, ALPS and FSALPS dominated canonical GP in evolving smaller but efficient trees with less bloat expressions. FSALPS significantly outperformed canonical GP and ALPS and some reported feature selection strategies in related literature on dimensionality reduction.

Feature Selection and Classification Using Age Layered Population Structure Genetic Programming

The curse of dimensionality is a major problem in the fields of machine learning, data mining and knowledge discovery. Exhaustive search for the most optimal subset of relevant features from a high dimensional dataset is NP hard. Sub–optimal population based stochastic algorithms such as GP and GA are good choices for searching through large search spaces, and are usually more feasible than exhaustive and determinis- tic search algorithms. On the other hand, population based stochastic algorithms often suffer from premature convergence on mediocre sub–optimal solutions. The Age Layered Population Structure (ALPS) is a novel meta–heuristic for overcoming the problem of premature convergence in evolutionary algorithms, and for improving search in the fitness landscape. The ALPS paradigm uses an age–measure to control breeding and competition between individuals in the population. This thesis uses a modification of the ALPS GP strategy called Feature Selection ALPS (FSALPS) for feature subset selection and classification of varied supervised learning tasks. FSALPS uses a novel frequency count system to rank features in the GP population based on evolved feature frequencies. The ranked features are translated into probabilities, which are used to control evolutionary processes such as terminal–symbol selection for the construction of GP trees/sub-trees. The FSALPS meta–heuristic continuously refines the feature subset selection process whiles simultaneously evolving efficient classifiers through a non–converging evolutionary process that favors selection of features with high discrimination of class labels. We investigated and compared the performance of canonical GP, ALPS and FSALPS on high–dimensional benchmark classification datasets, including a hyperspectral image. Using Tukey’s HSD ANOVA test at a 95% confidence interval, ALPS and FSALPS dominated canonical GP in evolving smaller but efficient trees with less bloat expressions. FSALPS significantly outperformed canonical GP and ALPS and some reported feature selection strategies in related literature on dimensionality reduction.

Amélioration de l'exactitude de l'inférence phylogénomique

L’explosion du nombre de séquences permet à la phylogénomique, c’est-à-dire l’étude des liens de parenté entre espèces à partir de grands alignements multi-gènes, de prendre son essor. C’est incontestablement un moyen de pallier aux erreurs stochastiques des phylogénies simple gène, mais de nombreux problèmes demeurent malgré les progrès réalisés dans la modélisation du processus évolutif. Dans cette thèse, nous nous attachons à caractériser certains aspects du mauvais ajustement du modèle aux données, et à étudier leur impact sur l’exactitude de l’inférence. Contrairement à l’hétérotachie, la variation au cours du temps du processus de substitution en acides aminés a reçu peu d’attention jusqu’alors. Non seulement nous montrons que cette hétérogénéité est largement répandue chez les animaux, mais aussi que son existence peut nuire à la qualité de l’inférence phylogénomique. Ainsi en l’absence d’un modèle adéquat, la suppression des colonnes hétérogènes, mal gérées par le modèle, peut faire disparaître un artéfact de reconstruction. Dans un cadre phylogénomique, les techniques de séquençage utilisées impliquent souvent que tous les gènes ne sont pas présents pour toutes les espèces. La controverse sur l’impact de la quantité de cellules vides a récemment été réactualisée, mais la majorité des études sur les données manquantes sont faites sur de petits jeux de séquences simulées. Nous nous sommes donc intéressés à quantifier cet impact dans le cas d’un large alignement de données réelles. Pour un taux raisonnable de données manquantes, il appert que l’incomplétude de l’alignement affecte moins l’exactitude de l’inférence que le choix du modèle. Au contraire, l’ajout d’une séquence incomplète mais qui casse une longue branche peut restaurer, au moins partiellement, une phylogénie erronée. Comme les violations de modèle constituent toujours la limitation majeure dans l’exactitude de l’inférence phylogénétique, l’amélioration de l’échantillonnage des espèces et des gènes reste une alternative utile en l’absence d’un modèle adéquat. Nous avons donc développé un logiciel de sélection de séquences qui construit des jeux de données reproductibles, en se basant sur la quantité de données présentes, la vitesse d’évolution et les biais de composition. Lors de cette étude nous avons montré que l’expertise humaine apporte pour l’instant encore un savoir incontournable. Les différentes analyses réalisées pour cette thèse concluent à l’importance primordiale du modèle évolutif.

Facebook et la réalité des amis virtuels

La dernière décennie fut marquée par l’avènement des sites de réseautage social ouvrant la voie à une nouvelle façon de communiquer. Avec 900 millions d’utilisateurs, Facebook est de loin le plus populaire de ces sites (Facebook, 2013). Les caractéristiques propres à cette plateforme, telles que l’information présente en ligne de même que la nature publique des interactions, imposent une réflexion sur son potentiel social. Nombre d’auteurs suggèrent que l’utilisation de Facebook pourrait mener à une augmentation du capital social et plus précisément du capital social de type bridging. Basée sur cette théorisation du réseau social établie par Putnam (2001), cette recherche s’est interrogée sur la participation de Facebook à la restructuration du réseau social chez les jeunes universitaires. Ainsi, 176 étudiants nouvellement arrivés à l’Université de Montréal furent interrogés à l’aide d’un questionnaire et d’entrevues. Cette façon de procéder permit de comparer les interactions que les étudiants ont en ligne aux interactions qu’ils ont en face-à-face. Il ressort de cette recherche que Facebook permet de fixer les liens sociaux naissants et facilite la formation de groupes dans un nouvel environnement. De plus, l’utilisation de cette plateforme accompagne le jeune tout au long de son parcours social et s’inscrit ainsi dans un processus évolutif.

Sociétés de fictions

Le concept des Sociétés de fictions élaboré dans le cadre de ce mémoire vise l’exploration de la médiation à l’ère du numérique. Pour penser les modalités de fictions littéraires avec l’idée qu’elles puissent former des sociétés distinctes, ce travail d’analyse propose d’examiner diverses fictions, plus précisément des expressions gothiques américaines en littérature contemporaine, afin d’en extraire un mode de pensée significatif. Dans le dessein d’analyser la manière dont ces fictions se relient entre elles, cette recherche se focalise sur le rapport qu’entretient la fiction littéraire avec la technologie ainsi qu’avec divers modes de diffusion et de médiation. Afin de comprendre comment les mécanismes du discours positionnent des œuvres de fictions les unes par rapport aux autres, ces fictions individuées seront d’abord examinées au sein d’une société qui leur est propre. Ceci mènera à exposer en quoi et comment les rapports qu’entretient l’humain avec la littérature et la technologie se reconfigurent par le biais de nouvelles formes de médiations. La présente réflexion se penche ainsi sur les modes d’interactions des fictions qui s’organisent en sociétés afin de pouvoir analyser comment le glissement du paradigme de l’imprimé et des supports matériels, à l’âge du numérique, peut se traduire par une manière inédite de penser notre relation au littéraire. En somme, cette réflexion sur la mobilité des formes et des plateformes liées aux fictions et à leur société devrait permettre de mieux analyser les individus qui inventent et consomment ces fictions, leur univers social ainsi que leur rapport intime à la technologie et ses médiations. Ces sociétés de fictions deviennent alors une clé pour comprendre notre rapport à la virtualisation de nos univers sociaux. Entre les sociétés de fictions et les sociétés des Hommes se noue un lien substantiel laissant entrevoir une véritable co-évolution de ces univers distincts. Les principales œuvres de fiction étudiées et citées seront celles du romancier et scénariste américain Bret Easton Ellis, plus précisément les romans Less Than Zero et Imperial Bedrooms. Il sera également question de la série télévisuelle Twin Peaks, diffusée sur la chaîne ABC en 1990 et réalisée par David Lynch, ainsi que d’une nouvelle de John Cheever, The enormous radio, parue en 1947, dans le New Yorker.

Molecular genetic characterization of endemic red -tailed barb,Gonoproktoptems curmuca (Hamilton - Buchanan, 1807)

The family Cyprinidae is the largest of freshwater fishes and, with the possible exception of Gobiidae, the largest family of vertebrates.Various members of this family are important as food fish, as aquarium fish, and in biological research. In this study, a fish species from this family exclusively found in the west flowing rivers originating from the Western Ghat region — Gonoproktopterus curmuca — was taken for population genetic analysis.There was an urgent need for restoration ecology by the development of apt management strategies to exploit resources judiciously. One of the strategies thus developed for the scientific management of these resources was to identify the natural units of the fishery resources under exploitation (Altukov, 1981). These natural units of a species can otherwise be called as stocks. A stock can be defined as a panmictic population of related individuals within a single species that is genetically distinct from other such populations.It is believed that a species may undergo micro evolutionary process and differentiate into genetically distinct sub-populations or stocks in course of time, if reproductively and geographically isolated.In recent times, there has been a wide spread degradation of natural aquatic environment due to anthropogenic activities and this has resulted in the decline and even extinction of some fish species. In such situations, evaluation of the genetic diversity of fish resources assumes important to conservation.The species selected for the study, was short-listed as one of the candidates for stock-specific, propagation assisted rehabilitation and management programme in rivers where it is naturally distributed. In connection with this, captive breeding and milt cryopreservation techniques of the species have been developed by the National Bureau of Fish Genetic Resources, Lucknow. However, for a scientific stock-specific rehabilitation programme, information on the stock structure and basic genetic profile of the species are essential and that is not available in case of G. curmuca. So the present work was taken up to identify molecular genetic markers like allozymes, microsatellites and RAPDs and, to use these markers to discriminate the distinct populations of the species, if any, in areas of its natural distribution. The genetic markers were found to be powerful tools to analyze the population genetic structure of the red-tailed barb and demonstrated clear cut genetic differentiation between pairs of populations examined. Geographic isolation by land distance is likely to be the factor that contributed to the restricted gene flow between the river systems. So the present study emphasizes the need for stock-wise, propagation assisted-rehabilitation of the natural populations of red-tailed barb, Gonoprokfopterus curmuca.

Designing in the real world is complex anyway - so what?

Designing is a heterogeneous, fuzzily defined, floating field of various activities and chunks of ideas and knowledge. Available theories about the foundations of designing as presented in "the basic PARADOX" (Jonas and Meyer-Veden 2004) have evoked the impression of Babylonian confusion. We located the reasons for this "mess" in the "non-fit", which is the problematic relation of theories and subject field. There seems to be a comparable interface problem in theory-building as in designing itself. "Complexity" sounds promising, but turns out to be a problematic and not really helpful concept. I will argue for a more precise application of systemic and evolutionary concepts instead, which - in my view - are able to model the underlying generative structures and processes that produce the visible phenomenon of complexity. It does not make sense to introduce a new fashionable meta-concept and to hope for a panacea before having clarified the more basic and still equally problematic older meta-concepts. This paper will take one step away from "theories of what" towards practice and doing and try to have a closer look at existing process models or "theories of how" to design instead. Doing this from a systemic perspective leads to an evolutionary view of the process, which finally allows to specify more clearly the "knowledge gaps" inherent in the design process. This aspect has to be taken into account as constitutive of any attempt at theory-building in design, which can be characterized as a "practice of not-knowing". I conclude, that comprehensive "unified" theories, or methods, or process models run aground on the identified knowledge gaps, which allow neither reliable models of the present, nor reliable projections into the future. Consolation may be found in performing a shift from the effort of adaptation towards strategies of exaptation, which means the development of stocks of alternatives for coping with unpredictable situations in the future.