Scientific computing is used frequently in an increasing number of disciplines to accelerate scientific discovery. Many such computing problems involve the numerical solution of partial differential equations (PDE). In this thesis we explore and develop methodology for high-performance implementations of PDE solvers for shared-memory multiprocessor architectures. We consider three realistic PDE settings: solution of the Maxwell equations in 3D using an unstructured grid and the method of conjugate gradients, solution of the Poisson equation in 3D using a geometric multigrid method, and solution of an advection equation in 2D using structured adaptive mesh refinement. We apply software optimization techniques to increase both parallel efficiency and the degree of data locality. In our evaluation we use several different shared-memory architectures ranging from symmetric multiprocessors and distributed shared-memory architectures to chip-multiprocessors. For distributed shared-memory systems we explore methods of data distribution to increase the amount of geographical locality. We evaluate automatic and transparent page migration based on runtime sampling, user-initiated page migration using a directive with an affinity-on-next-touch semantic, and algorithmic optimizations for page-placement policies. Our results show that page migration increases the amount of geographical locality and that the parallel overhead related to page migration can be amortized over the iterations needed to reach convergence. This is especially true for the affinity-on-next-touch methodology whereby page migration can be initiated at an early stage in the algorithms. We also develop and explore methodology for other forms of data locality and conclude that the effect on performance is significant and that this effect will increase for future shared-memory architectures. Our overall conclusion is that, if the involved locality issues are addressed, the shared-memory programming model provides an efficient and productive environment for solving many important PDE problems.

No description available.

La morphogenèse des plantes repose sur deux mécanismes cellulaires : la division et l'élongation. Par ailleurs, la croissance est source de contraintes mécaniques qui affectent les cellules et guident la morphogenèse. Si les contraintes mécaniques influencent l'orientation du plan de division dans les cellules animales, rien n'est prouvé pour les cellules végétales. À l'heure actuelle, la forme de la cellule est proposée comme le facteur principal gouvernant l'orientation du plan dans les divisions symétriques : les cellules se divisent selon un des plans les plus courts. Cette règle géométrique a été validée dans des tissus à croissance ou courbure isotropes, mais les mécanismes moléculaires sous-jacents demeurent inconnus. Dans cette thèse, un pipeline a été mis au point pour analyser les divisions cellulaires dans les différents domaines du méristème apical caulinaire d'Arabidopsis thaliana et questionner l'application de la règle géométrique dans ce tissu. La zone frontière du méristème présente une proportion anormalement basse de plans de division très courts. Des simulations de tissus en croissance, dans lesquelles une règle de division mécanique a été implémentée, ont montrées le même biais sur les orientation des plans, comparé à la règle géométrique. Des ablations laser de quelques cellules de l'épiderme ont également été effectuées afin de perturber localement le patron de contraintes mécaniques. Les résultats montrent que l'orientation du plan des divisions postérieures à cette perturbation suit le nouveau patron de contraintes. Enfin, une nouvelle méthode quantitative, basée sur l'utilisation d'un micro-indenteur, a été mise au point pour quantifier la réponse du cytosquelette, et en particulier des microtubules, aux contraintes mécaniques. Le protocole de compression a été testé et validé sur les mutants katanin et spiral2, dans lesquels la réponse aux contraintes est respectivement faible ou amplifiée. / Morphogenesis during primary plant growth is driven by cell division and elongation. In turn, growth generates mechanical stress, which impacts cellular events and channels morphogenesis. Mechanical stress impacts the orientation of division plane in single animal cells; this remains to be fully demonstrated in plants. Currently, cell geometry is proposed to be the main factor determining plane orientation in symmetric divisions: cell divide along one the shortest paths. This geometrical rule was tested on tissues with rather isotropic shapes or growth and the corresponding molecular mechanism remains unknown, although it could involve tension within the cytoskeleton. To address these shortcomings, we developed a pipeline to analyze cell divisions in the different domains of the shoot apical meristem of Arabidopsis thaliana. We computed the probability of each possible planes according to cell geometry and compared the output to observed orientations. A quarter of the cells did not follow the geometrical rule. Boundary domain was enriched in long planes aligned with supracellular maximal tension lines. Computer simulations of a growing tissue following a division rule that relies on tension gave the most realistic outputs. Mechanical perturbations of local stress pattern, by laser ablations, further confirmed the importance of mechanical stress in cell division. To explore the role of microtubules in this process, we developed a microindenter-based protocol to quantify the cytoskeletal response to mechanical stress. This protocol was tested and validated in the katanin and spiral2 mutants, in which the response to stress is delayed or promoted respectively.

As bromélias são valorizadas por suas características ornamentais, sendo o gênero Vriesea representativo neste setor. O aprimoramento de métodos de propagação in vitro destas plantas é altamente necessário a fim de suprir as necessidades do mercado, e evitar o extrativismo ilegal. Nesse contexto, o presente trabalho objetivou aprimorar o protocolo de propagação in vitro de espécies do gênero Vriesea, bem como aumentar o conhecimento global das espécies em estudo. Para tanto, sementes das espécies V. carinata, V. friburgensis, V. paraibica e V. simplex foram submetidas a processos de assepsia e introduzidas in vitro sob três temperaturas: 22 °C, 27 °C e 32 °C. Paralelamente, sementes das mesmas espécies foram semeadas em bandejas e mantidas em casa de vegetação. Através da microscopia eletrônica de varredura e ótica foi realizada a descrição morfo-anatômica do desenvolvimento pós-seminal das plântulas das mesmas espécies. Além disso, procurou-se adequar o meio de cultura às necessidades das mesmas espécies e de V. hieroglyphica, sendo testadas 3 doses de nitrogênio e 3 doses de magnésio. Também procurou-se avaliar a taxa de sobrevivência durante o processo de aclimatização de plântulas das espécies de Vriesea mencionadas (com exceção de V. hieroglyphica). Objetivou-se comparar características anatômicas e morfológicas de folhas das referidas espécies cultivadas in vitro e em casa de vegetação. Por fim, com o objetivo de estabelecer um protocolo de micropropagação para as espécies Vriesea carinata, V. paraibica, V. phillipo-coburgii; V. simplex e Aechmea nudicaulis, foram introduzidos in vitro explantes somáticos, após testes de assepsia. A partir dos experimentos citados foi verificado que a temperatura exerce uma forte influência nas taxas de germinação e mortalidade das sementes de Vrieseas in vitro, sendo que a temperatura de 32°C proporcionou as maiores taxas de mortalidade, mostrando-se prejudicial ao sucesso reprodutivo. A germinação em casa de vegetação apresentou altas taxas de mortalidade e taxas de germinação mais baixas do que in vitro. A descrição morfo-anatômica do desenvolvimento pós-seminal permitiu a caracterização de cinco estágios de desenvolvimento. Com relação ao experimento de nutrição mineral, foi evidenciado que as doses de nitrogênio e magnésio testadas acarretaram em menor acúmulo de cálcio e de potássio nas plantas, sendo que esse fato resultou em menor acúmulo de massa fresca. O experimento de aclimatização ficou inviabilizado devido ao ataque às plântulas por praga Fungus Gnats. Com a análise morfo-anatômica das folhas de plantas cultivadas in vitro e em casa de vegetação foi possível observar a presença de estruturas típicas de Bromeliaceae nas plantas cultivadas em ambas as condições: estômatos, tricomas escamiformes, mesofilo com epiderme unisseriada, parênquima aqüífero, feixes colaterais fechados e canais de aeração. Com relação à introdução in vitro a partir de explantes somáticos, pode-se afirmar que o uso de cefotaxima apresentou uma boa eficiência no combate à contaminação bacteriana em cultura de ápices caulinares. A escolha de ápice vegetativo de brotos laterais como explantes iniciais para a cultura das referidas espécies in vitro é uma boa opção. A otimização da propagação destas espécies in vitro poderá diminuir a pressão extrativista que estas vêm sofrendo e, ao mesmo tempo, abastecer o mercado ornamental / Bromeliads are valued for their ornamental characteristics and the genus Vriesea is representative in this sector. The improvement of in vitro propagation of these plants is highly necessary in order to meet market needs, and, at the same time, to prevent illegal extraction of this plants from their natural habitat. In this context, this study aimed to improve the protocol for in vitro propagation of species of Vriesea and increase the global knowledge of these by morpho-anatomical characterization of the development of the seedling and leaf. Seeds of V. carinata, V. friburgensis, V.paraiba and V. simplex were submitted to aseptic procedures and introduced in vitro under three temperatures: 22 ° C, 27 ° C and 32 ° C. Additionaly, seeds of these species were sown in trays and maintained in a greenhouse. The post-seminal development was described by light and scanning electron microscopy. In addition, the adjustment of the culture medium for these four species and V. hieroglyphica was tested, by testing three doses of nitrogen combined with three doses of magnesium. The acclimatization efficiency of these Vriesea species, except for V. hieroglyphica, after a prior culture in the presence and absence of IBA was done, in three commercial substrates to verify IBA effect in rooting and seedling survival. This study also aimed to compare anatomical and morphological characteristics of leaves of the species cultivated in vitro and in the greenhouse. Finally, in order to establish a micropropagation protocol for the species Vriesea carinata, V. paraiba, V. phillipo-coburgii; V. simplex and Aechmea nudicaulis, somatic explants were introduced in vitro after sterilization tests. From all the experiments cited it was observed that the temperature strongly influences germination and mortality rates of Vriesea germinating seeds in vitro. The temperature of 32 ° C provided the highest mortality rates, being harmful to the reproductive success of this species. The germination in the greenhouse showed higher mortality and lower germination rates than in vitro germination. The morpho-anatomical description of the post-seminal development allowed for the characterization of five stages of development. With regard to the mineral nutrition experiment, the doses of nitrogen and magnesium tested resulted in less accumulation of calcium and potassium in plants, resulting in less accumulation of fresh weight. The acclimatization experiment was lost by the attack of Fungus gnats. With the morpho-anatomical analysis of leaves of plants grown in vitro and in the greenhouse it was possible to observe the presence of typical structures of Bromeliaceae such as stomata, scales, mesophyll with uniseriate epidermis, water storage tissue, collateral vascular bundles and air channels. Finally, the use of cefotaxime proved efficient against bacterial contamination in in vitro establishment of shoot apex explants in vitro. The choice of shoot apices from lateral buds as initial explants for in vitro establishment of those species was a good alternative. Optimization of in vitro propagation of bromeliad species can reduce their extractivism pressure and, at the same time, supply the ornamental plant market

En se développant, les plantes produisent des organes le long des tiges suivant des organisations stéréotypées, appelées phyllotaxies. Ces structures se forment dans les méristèmes, qui abritent une niche de cellules souches : les organes y sont produits successivement et leur positionnement dépendrait d'interactions dynamiques avec les organes pré-existants. Ces interactions seraient notamment dues à des champs inhibiteurs générés par le transport polaire de l'hormone végétale auxine. Afin de rechercher si d'autres facteurs que l'auxine contrôlent la phyllotaxie chez Arabidopsis thaliana, nous nous sommes intéressés au rôle possible des cytokinines, une autre hormone végétale. Nous avons développé des nouvelles méthodes statistiques pour analyser la structure de la phyllotaxie. Cette approche nous a permis d'identifier des anomalies de phyllotaxie chez des plantes mutantes pour le gène AHP6 (ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER protein 6), un inhibiteur de la signalisation des cytokinines. Notre analyse suggérait des possibles perturbations du plastochrone, la période de temps séparant l'initiation de deux organes, ce que nous avons alors confirmé par imagerie confocale en temps réel. Nos données montrent que AHP6 contrôle la régularité du plastochrone, et suggèrent que les perturbations de phyllotaxies sont dues à l'initiation simultanée de deux à trois organes dans le méristème. De plus, AHP6 est exprimé dans les organes et sa protéine établit des champs qui inhibent la signalisation des cytokinines au delà des organes. Pour mieux comprendre les rôles possibles de ces champs, nous avons généré un modèle numérique théorique de la phyllotaxie. Notre étude suggère que le plastochrone pourrait être déstabilisé par du bruit affectant le seuil d'activation nécessaire aux cellules méristématiques pour se différencier en organe. Des champs inhibiteurs pourraient filtrer les effets de ce bruit en influant sur la cinétique d'émergence des organes. Les propriétés observées des champs de AHP6 sont en accord avec ce modèle et nos données expérimentales suggèrent en effet que AHP6 et les cytokinines peuvent moduler la signalisation auxine lors de l'émergence des organes. Nous proposons comme modèle que le transport et la signalisation de l'auxine positionnent de manière robuste les organes mais génèrent un plastochrone irrégulier en présence de bruit. Des champs inhibiteurs de cytokinines stabiliseraient le plastochrone, assurant un couplage plus robuste entre le temps et l'espace lors de l'établissement de la phyllotaxie. / During development, plant aerial organs are produced along the stems following stereotyped patterns. This so-called phyllotaxis is initiated at the shoot meristem, which contains the stem cell niche: organs are produced iteratively and their precise position is thought to depend on dynamic interactions with preexisting organs. These interactions would notably result from inhibitory fields generated by the polar transport of the plant hormone auxin. To investigate whether other factors than auxin regulate phyllotaxis, we studied the potential role of cytokinin signaling. We developed a new pipeline of methods based on statistics to analyze phyllotactic patterns. This approach allowed us to identify phyllotactic perturbations in mutants of the AHP6 (ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER protein 6), an inhibitor of cytokinin signaling that suggested perturbations in the plastochron, the time between two organ initiations. This was further confirmed using confocal live-imaging. We demonstrated that AHP6 controls the regularity of the plastochron, and our results suggest that the defective phyllotaxis in ahp6 is caused by concomitant initiations of two or three organs in the meristem. Interestingly, AHP6 is expressed in organs and the protein can move beyond these domains, generating cytokinin signaling inhibitory fields. To explore further the putative role of these secondary fields, we generated a mathematical model of phyllotaxis. This suggested that plastochron instabilities could be caused by noise affecting the threshold at which meristematic cells are recruited into organs. Inhibitory fields generated by AHP6 could filter out the effect of noise by modifying the kinetics of early organ emergence. Consistently, the properties of AHP6 fields fit the model predictions and our experimental data show that AHP6 and cytokinin modulate auxin signaling during organ emergence. We thus propose a model in which auxin transport and signaling robustly control organ positioning but generates plastochron instablities in noisy backgrounds. In this scenario cytokinin inhibitory fields would stabilize the rhythmicity of organ initiation, ensuring a robust coupling of space and time during pattern formation.

Tesis por compendio / [EN] Cannabis sativa L. (Cannabaceae) is an angiosperm, allogamous and dicotyledonous species that includes short and neutral-day varieties with dioecious specimens (males and females), and monoecious plants. Among its many applications, its industrial and medicinal uses stand out. Despite the fact that cannabis has been used by humans since ancient times and the growing interest that the C. sativa therapeutic properties have aroused in researchers around the world, the psychoactivity of some of its varieties, derived from its ¿9-tetrahydrocannabinol (THC) content, has motivated the prohibition of its cultivation for almost sixty years. The strict control to which cannabis has been subjected has prevented professionals from all over the world from carrying out genetic breeding programs for this species, which has resulted in the absence of uniform varieties. In this Doctoral Thesis, different biotechnological tools for cannabis genetic improvement have been developed. In the first place, given the lack of reproducibility of some cannabis plant in vitro regeneration protocols and the great influence that the genotype exerts on their effectiveness, plant in vitro regeneration competence of different explants was evaluated. As a result, an hormone-free protocol from C. sativa hypocotyls that presents high regeneration rates (ranging from 32.26% to 71.15%) in all the genotypes evaluated, also presenting a 17.94% of spontaneous rooting rate of regenerants has been developed. At the same time, the polysomatic pattern of different cannabis explants has been studied, and it has been possible to regenerate, from them, a significant percentage of mixoploid specimens (17.65% from cotyledons and 13.33% from hypocotyls) that, as described in the existing literature, could show a greater capacity for cannabinoid synthesis. On the other hand, given the absence of scientific publications in this regard, and the potential that this technique presents to alleviate the intrinsic variability of this species, the most in-depth study to date on the male floral biology of C. sativa has been developed. Up to 476,903 microspores and pollen grains per male flower, with in vivo microspore viability rates from 53.71 to 70.88% have been found. Furthermore, all stages of development of the microgametophyte have been correlated with an easily measurable floral morphological marker such as the bud length, identifying bud length intervals containing mostly vacuolate microspores and young bi-cellular pollen grains in all the phenotypes evaluated. In this way, and although the starch presence in C. sativa microspores and pollen grains follows a similar pattern to that observed in species recalcitrant to androgenesis, it has been possible to address the induction of microspore embryogenesis in this species, obtaining for the first time microspore-derived multicellular structures after one week long cold-shock bud pretreatment. Finally, as a prerequisite for the genetic editing of C. sativa by using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas systems, and taking advantage of the in vitro plant regeneration protocol which resulted from this Doctoral Thesis, it has been possible to develop for the first time a protocol for the production of stably transformed cannabis plants, which represents a historical milestone in the genetic improvement of the species. After co-culture with A. tumefaciens and subsequent culture in antibiotic-containing selective regeneration medium, hypocotyls achieved 23.1% and 5.0% of regeneration and transformation rates respectively. As a whole, the present Doctoral Thesis provides a range of biotechnological tools that will allow the development of a new generation of high-yield cannabis varieties with uniform traits, resistant to multiple biotic and abiotic stresses, and therefore being suitable for both industrial and medicinal use. / [ES] Cannabis sativa L. (Cannabaceae) es una especie angiosperma, alógama y dicotiledónea compuesta por variedades de día corto y día neutro que presentan ejemplares dioicos (machos y hembras), y plantas monoicas. Entre sus múltiples aplicaciones destacan tanto su uso industrial como su uso medicinal. A pesar de que el cannabis ha sido empleado por el ser humano desde tiempos ancestrales, la psicoactividad que presentan algunas de sus variedades, derivada de su contenido en ¿ 9 -tetrahidrocannabinol (THC), ha motivado la prohibición de su cultivo durante casi sesenta años. La estricta fiscalización a la que ha sido sometido el cannabis, ha impedido llevar a cabo programas de mejora genética de esta especie, lo que se ha traducido en la ausencia de variedades uniformes. En esta Tesis Doctoral se han desarrollado diferentes herramientas biotecnológicas para la mejora genética del cannabis. En primer lugar, dada la falta de reproducibilidad de algunos protocolos de cultivo in vitro de cannabis y la gran influencia que el genotipo ejerce en la efectividad de los mismos, se evaluó la capacidad de regeneración in vitro de diferentes explantes. Como resultado, se ha desarrollado un protocolo libre de hormonas a partir de hipocótilos de C. sativa que presenta altas tasas de regeneración (las cuales oscilan del 32,26% al 71,15%) en todos los genotipos evaluados, presentando además un 17,94% de tasa de enraizado espontáneo de los regenerantes. A su vez, se ha estudiado el patrón polisomático de diferentes explantes de cannabis y se ha conseguido regenerar, a partir de los mismos, un porcentaje significativo de ejemplares mixoploides (17,65% procedentes de cotiledones y 13,33% de hipocotilos) que, tal y como describe la bibliografía existente, podrían mostrar una mayor capacidad de síntesis de cannabinoides. Por otro lado, dada la ausencia de publicaciones científicas al respecto y el potencial que esta técnica presenta para paliar la variabilidad intrínseca de esta especie, se ha desarrollado el estudio más profundo hasta la fecha relativo a la biología floral masculina de C. sativa. Se han descrito hasta 476.903 microsporas y granos de polen por flor masculina, con tasas de viabilidad in vivo de las microsporas del 53,71 al 70,88%. Además, se han correlacionado todas las etapas de desarrollo del microgametofito con la longitud de la yema, identificando intervalos de longitud de yema que contienen mayoritariamente microsporas vacuoladas y granos de polen joven bicelular en todos los fenotipos evaluados. De este modo, y aunque la presencia de almidón en las microsporas y granos de polen de C. sativa sigue un patrón similar al observado en especies recalcitrantes a la androgénesis, ha sido posible abordar la inducción de la embriogénesis de microsporas en esta especie, consiguiendo producir por primera vez estructuras multicelulares derivadas de las microsporas tras aplicar sobre las yemas un pretratamiento de frío de una semana de duración. Finalmente, como requisito previo para la edición genética de C. sativa mediante los sistemas CRISPR/Cas, y haciendo uso del protocolo de regeneración in vitro de plantas surgido de la presente Tesis Doctoral, se ha conseguido desarrollar por primera vez un protocolo para producir plantas de cannabis transformadas genéticamente de forma estable, lo que supone un hito histórico en la mejora genética de la especie. Después del cocultivo con A. tumefaciens y el posterior cultivo en medio de regeneración selectiva con antibióticos, los hipocótilos lograron respectivamente un 23,1% y un 5,0% de tasas de regeneración y transformación. En su conjunto, la presente Tesis Doctoral proporciona un abanico de herramientas biotecnológicas que permitirán el desarrollo de una nueva generación de variedades de cannabis de alto rendimiento, que presenten caracteres homogéneos, resistentes a múltiples estreses tanto bióticos como abióticos, y siendo así aptas tanto para un uso industrial como medicinal. / [CAT] Cannabis sativa L. (Cannabaceae) és una espècie angiosperma, alógama i dicotiledònia composta per varietats de dia curt i dia neutre que presenten exemplars dioics (mascles i femelles), i plantes monoiques. Entre les seues múltiples aplicacions destaquen tant el seu ús industrial com el seu ús medicinal. Tot i que el cànnabis ha sigut emprat per l'ésser humà des de temps ancestrals, la psicoactivitat que presenten algunes de les seues varietats, derivada del seu contingut en ¿9-tetrahidrocannabinol (THC), ha motivat la prohibició del seu cultiu durant gairebé seixanta anys. L'estricta fiscalització a la qual ha sigut sotmés el cànnabis, ha impedit que professionals de tot el món puguen dur a terme programes de millora genètica d'aquesta espècie, la qual cosa s'ha traduït en l'absència de varietats uniformes. En aquesta Tesi Doctoral s'han desenvolupat diferents eines biotecnològiques per a la millora genètica del cànnabis. En primer lloc, donada la falta de reproducibilitat d'alguns protocols de cultiu in vitro de cànnabis i la gran influència que el genotip exerceix en l'efectivitat d'aquests, es va avaluar la capacitat de regeneració in vitro de diferents explants. Com a resultat, s'ha desenvolupat un protocol lliure d'hormones a partir de hipocòtils de C. sativa que presenta altes taxes de regeneració (les quals oscil·len del 32,26% al 71,15%) en tots els genotips avaluats, presentant a més un 17,94% de taxa d'arrelat espontani dels regenerants. Al mateix temps, s'ha estudiat el patró polisomàtic de diferents explants de cànnabis i s'ha aconseguit regenerar, a partir d'aquests, un percentatge significatiu d'exemplars mixoploids (17,65% procedents de cotilèdons i 13,33% de hipocòtils) que, tal com descriu la bibliografia existent, podrien mostrar una major capacitat de síntesi de cannabinoids. D'altra banda, donada l'absència de publicacions científiques sobre aquest tema i el potencial que aquesta tècnica presenta per a pal·liar la variabilitat intrínseca d'aquesta espècie, s'ha desenvolupat l'estudi més profund fins hui relatiu a la biologia floral masculina de C. sativa. S'han descrit fins a 476.903 microspores i grans de pol·len per flor masculina, amb taxes de viabilitat in vivo de les microspores del 53,71 al 70,88%. A més, s'han correlacionat totes les etapes de desenvolupament del microgametòfit amb la longitud de la gemma, identificant intervals de longitud de gemma que contenen majoritàriament microspores vacuolades i grans de pol·len jove bi-cel·lular en tots els fenotips avaluats. D'aquesta manera, i encara que la presència de midó en les microspores i grans de pol·len de C. sativa segueix un patró similar a l'observat en espècies recalcitrants a la androgènesi, ha sigut possible abordar la inducció de la embriogènesi de microspores en aquesta espècie, aconseguint produir per primera vegada estructures multicel·lulars derivades de les microspores després d'aplicar sobre les gemmes un pretractament de fred d'una setmana de duració. Finalment, com a requisit previ per a l'edició genètica de C. sativa mitjançant els sistemes CRISPR/Cas, i fent ús del protocol de regeneració in vitro de plantes sorgit de la present Tesi Doctoral, s'ha aconseguit desenvolupar per primera vegada un protocol per a produir plantes de cànnabis transformades genèticament de manera estable, la qual cosa suposa una fita històrica en la millora genètica de l'espècie. Després del cocultiu amb A. tumefaciens i el posterior cultiu en medi de regeneració selectiva amb antibiòtics, els hipocòtils van aconseguir respectivament un 23,1% i un 5,0% de taxes de regeneració i transformació. En el seu conjunt, la present Tesi Doctoral proporciona un ventall d'eines biotecnològiques que permetran el desenvolupament d'una nova generació de varietats de cànnabis d'alt rendiment, que presenten caràcters homogenis, resistents a múltiples estressos tant biòtics com abiòtics, i sent així aptes tant per a un ús industrial com medicinal. / Galán Ávila, A. (2021). Development of biotechnological tools for the genetic improvement of Cannabis sativa L [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/176013 / TESIS / Compendio

Le développement d’un organisme multicellulaire requière la coordination de la croissance, détermination tissulaire et différenciation cellulaire. Cependant, alors que les bases de la génétique de la morphogenèse ont été rigoureusement étudiées, le processus permettant la conversion de l’activité génétique en des structures biologiques complexes est bien moins compris. Chez Arabidopsis thaliana, les feuilles et fleurs initiés à partir du Méristème Apical Primaire (MAP) ont une expression génétique casi similaire. Toutefois, leur forme est considérablement différente dès les premières étapes de leur développement. Une compréhension de ce paradoxe requière avant tout de précisément quantifier la croissance dans toutes les dimensions de ces organes. Dans cet article, je présente une méthode de quantification spatio-temporelle complète de la croissance et de la prolifération des feuilles et des fleurs chez A. thaliana. En analysant des séries d’images confocales, j’en ai conclu que la différence morphologique observée entre feuilles et fleurs émerge principalement d’une asymétrie de la distribution de la croissance entre leurs côtés abaxial et adaxial, tôt dans leur développement. Je montre que le tissue contribuant principalement au développement des primordia est la couche 2 (L2) chez les feuilles et la couche 3 (L3) chez les fleurs. Mes résultats préliminaires démontrent que les premiers signes de l’initiation d’organes est un changement de distribution de la croissance, et non de la prolifération. Dans le futur, en appliquant, par exemple, cette méthodologie à l’étude de gènes de développement, il sera possible de finalement réconcilier la morphogenèse et la génétique de l’initiation des plantes. / The development of a multicellular organism requires the proper coordination of growth, pattern determination and cell differentiation. Still, while the genetic basis of morphogenesis has been extensively studied, the process converting gene activity into intricate biological shapes is less understood. In Arabidopsis thaliana, flowers and leaves, both initiated from the shoot apical meristem (SAM), have a very similar genetic expression profile. Yet, their shape differs considerably from early developmental stages. A full comprehension of this paradox requires an accurate quantification of cellular growth in those organs. In this paper, I am presenting a methodology for the complete spatio-temporal quantitative analysis of growth and proliferation of initiating leaves and flowers in wild type Arabidopsis thaliana. By analyzing time series of leaf and flower confocal images, I conclude that the morphological differences observed between flowers and leaves mainly arises from asymmetrical distributions of growth between their adaxial and abaxial sides during their initiation. I show that the tissue that mainly contributes to the development of early primordium is the layer 2 (L2) in leaves, and the layer 3 (L3) in flowers. My preliminary results also demonstrate that the first signs of organ initiation are a change in growth distribution, not cell proliferation. In the future, by applying this methodology, for example, to study morphogen reporter lines, it could finally bridge the gap between the morphogenesis and the genetics of plant initiation.

No description available.

Made available in DSpace on 2016-04-26T19:39:33Z (GMT). No. of bitstreams: 1 2007 - Sergio Trabali Camargo Filho.pdf: 4423367 bytes, checksum: 827592ba3f6a9d37da8d784b6ae6ffe8 (MD5) Previous issue date: 2009-12-18 / The environmental conditions of light, temperature and water availability, along with grazing, are major factors establishing growth and phenology of forage species. The climatic effects imprint dynamics specific to pasture ecosystems, which are generally referred as "seasonality of the pasture." This study was set in an area of Fragiudult soil, located in Serop?dica municipality, Rio de Janeiro State, Brazil. The experiment began with a cut to make uniform the pasture at the height of 0.05 m, in February 2002. The aim was to determine the influence of climatic and genotypes factors in the expression of features of production, also the partition of carbon and nutrients in the aerial and ground parts of the perennial grasses Cynodon nlemfuensis (stargrass Puerto Rico); Cynodon spp (Tifton-85 grass); Digitaria swazilandensis (swazi grass) and Digitaria decumbens cv. Transvala (Transvala grass). Two hypotheses were formulated to guide the study: i) in the drier periods of the year, the fodder allocate more carbon and nutrients in roots than in the aerial parts of the plants; ii) the species have more or less plasticity to respond to seasonal climatic fluctuations, and periodic defoliation, evidencing differential adaptive capabilities. To check these possibilities, it was used a simple strategy trial, where, from the cut for uniformity, there were evaluated eight periods, between 03/26/02 and 01/14/03, at intervals of 42 days, sampling material of aerial and root fitomass. After processing the samples, the fresh and air dry mass were determined (kg ha-1). In the root system, the accumulation and distribution of dry weight, and the length and surface area of roots to the depth of 1.0 m were determined, by sequential extraction of monoliths (1.0 dm3) from the wall of a soil trench. In sub-samples of dried and grinded aerial parts and roots, the levels of nitrogen, phosphorus, calcium and magnesium (g kg-1) were quantified. The results showed that: regardless of forage species, the root:shoot ratio (based on dry fitomass in standing fluctuated seasonally, with higher values in the dryer months of the year, and smaller in the months of highest rainfall; the species varied in their responses, evidencing the existence of phenotypic plasticity for attributes of production (accumulation of forage and root mass) and adaptive (length and specific root area), with the Tifton-85 grass outstanding by the level of productivity and stability; the magnitude of the differences between the species was controlled by the water availability, and it was amplified in the periods of increased rainfall and reduced in driest periods. The concentration of nutrients, in aerial and root biomass, responses were varied according to the nutrient, but, in general, the more nutrient concentrated in Digitaria that Cynodon, observation which was also valid for the quality of fiber. Already, the Cynodon accumulated more nutrients that Digitaria per unit area. For the relations of concentrations and accumulation of nutrients roots: shoot had little effect on the grasses and a rule, during dried periods was higher than those of rainfall period. Finally, each grass has its own dynamic in relations soil-plant-atmosphere, showing once again the different adaptive responses of these grasses. / As condi??es ambientais de luz, temperatura, disponibilidade h?drica e de nutrientes, junto com o pastejo, s?o os principais moduladores do crescimento e fenologia das esp?cies forrageiras. Os efeitos clim?ticos imprimem din?micas espec?ficas ao ecossistema pastoril, que s?o geralmente referidas como sazonalidade das pastagens . O presente trabalho foi realizado em uma ?rea de solo Planossolo, localizada no munic?pio de Serop?dica, RJ. O prop?sito foi o de determinar a influ?ncia dos fatores clim?ticos e genot?picos na express?o de caracter?sticas produtivas; assim como na parti??o de carbono e nutrientes entre as por??es a?reas e subterr?neas das gram?neas perenes Cynodon nlemfuensis (capim-Estrela Porto Rico); Cynodon spp (capim-Tifton-85); Digitaria swazilandensis (capim-su?zi) e Digitaria decumbens cv. Transvala (capim-Transvala). Foram formuladas duas hip?teses para orientar o trabalho: i) nos per?odos mais secos do ano, os capins alocam mais carbono e nutrientes nas ra?zes do que na parte a?rea; ii) os capins possuem maior ou menor plasticidade para responder ?s oscila??es clim?ticas sazonais e ? desfolha peri?dicas, evidenciando capacidades adaptativas diferenciais. Para verificar essas possibilidades, usou-se uma estrat?gia experimental simples, onde, a partir do corte de uniformiza??o, foram avaliados oito per?odos de crescimento, entre 26/03/02 e 14/01/03, a intervalos de 42 dias, com amostragens de fitomassa de parte a?rea e radicular. Ap?s processamento das amostras, foram determinadas a massa verde e massa seca da parte a?rea (kg ha-1). No sistema radicular, foram determinados o ac?mulo e a distribui??o da massa seca, al?m do comprimento e ?rea superficial das ra?zes at? a profundidade de 1,0 m, pela extra??o seq?encial de mon?litos (1,0 dm3) a partir da parede de uma trincheira de solo. Em sub-amostras secas e mo?das de parte a?rea e ra?zes foram determinados os teores de nitrog?nio, f?sforo, c?lcio e magn?sio (g kg-1). Os resultados obtidos permitiram observar que: independentemente do capim, a rela??o raiz: parte a?rea oscilou sazonalmente, tendo maiores valores nos meses mais secos do ano e menores nos meses de maior pluviosidade; os capins variaram as suas respostas, evidenciando a exist?ncia de plasticidade fenot?pica para atributos produtivos (ac?mulos de forragem e massa radicular) e adaptativos (comprimento espec?fico e ?rea radicular), tendo o capim-Tifton-85 se sobressa?do pelo n?vel de produtividade e estabilidade; a magnitude das diferen?as entre os capins foi controlada pela disponibilidade de ?gua, sendo amplificada nos per?odos de maior pluviosidade e reduzida nos per?odos mais secos. A concentra??o de nutrientes, tanto da fitomassa a?rea como da fitomassa radicular, tiveram respostas variadas de acordo com o nutriente, mas, de um modo geral, as Digitaria concentraram mais nutrientes que os Cynodon, observa??o que tamb?m foi v?lida para a qualidade da fibra. J?, os Cynodon acumularam mais nutrientes que as Digitaria por unidade de ?rea. Para as rela??es das concentra??es e ac?mulos de nutrientes ra?zes: parte a?rea teve poucos efeitos para os capins e, em geral no per?odo seco foram superiores aos dos per?odos chuvosos. Por fim, cada capim estabeleceu sua pr?pria din?mica nas rela??es solo-planta-atmosfera, evidenciando mais uma vez as diferentes respostas adaptativas destas gram?neas forrageiras.

Lolium perenne is one of the most important forage crops globally and in New Zealand. Lotus corniculatus is a dicotyledonous forage that contains valuable traits such as high levels of condensed tannins, increased digestibility, and high nitrogen fixing abilities. However, conventional breeding between these two forage crops is impossible due to their markedly different taxonomic origin. Protoplast fusion (somatic hybridisation) provides an opportunity for gene introgression between these two species. This thesis describes the somatic hybridisation, the regeneration and the molecular analysis of the putative somatic hybrid plants obtained between L. perenne and L. corniculatus. Callus and cell suspensions of different cultivars of L. perenne were established from immature embryos and plants were regenerated from the callus. Of the 10 cultivars screened, cultivars Bronsyn and Canon had the highest percentage of callus induction at 36% each on 5 mg/L 2,4-D. Removal of the palea and lemma which form the seed coat was found to increase callus induction ability of the embryos. Plant regeneration from the callus was achieved when the callus was plated on LS medium supplemented with plant growth regulators at different concentrations. Variable responses to shoot regeneration was observed between the different cultivars with the cv Kingston having the lowest frequency of shoot formation (12%). Different factors affecting the protoplast isolation of L. perenne were investigated. The highest protoplast yield of 10×10⁶ g⁻¹FW was obtained when cell suspensions were used as the tissue source, with enzyme combination 'A' (Cellulase Onozuka RS 2%, Macerozyme R-10 1%, Driselase 0.5%, Pectolyase 0.2%), for 6 h incubation period in 0.6 M mannitol. Development of microcolonies was only achieved when protoplasts were plated on nitrocellulose membrane with a L. perenne feeder layer on PEL medium. All the shoots regenerated from the protoplast-derived calli were albino shoots. The highest protoplast yield (7×10⁶ g⁻¹FW) of L. corniculatus was achieved from cotyledons also with enzyme combination 'A' (Cellulase Onozuka RS 2%, Macerozyme R-10 1%, Driselase 0.5%, Pectolyase 0.2%), for 6 h incubation period in 0.6 M mannitol. The highest plating efficiency for L. corniculatus of 1.57 % was achieved when protoplasts were plated on nitrocellulose membrane with a L. perenne feeder layer on PEL medium. The highest frequency of shoot regeneration (46%) was achieved when calli were plated on LS medium with NAA (0.1 mg/L) and BA (0.1 mg/L). Protoplast fusion between L. perenne and L. corniculatus was performed using the asymmetric somatic hybridisation technique using PEG as the fusogen. L. perenne protoplasts were treated with 0.1 mM IOA for 15 min and L. corniculatus protoplasts were treated with UV at 0.15 J/cm² for 10 min. Various parameters affecting the fusion percentage were investigated. Successful fusions were obtained when the fusions were conducted on a plastic surface with 35% PEG (3350 MW) for 25 min duration, followed by 100 mM calcium chloride treatment for 25 min. A total of 14 putative fusion colonies were recovered. Shoots were regenerated from 8 fusion colonies. Unexpectedly, the regenerated putative hybrid plants resembled L. corniculatus plants. The flow cytometric profile of the putative somatic hybrids resembled that of L. corniculatus. Molecular analysis using SD-AFLP, SCARs and Lolium specific chloroplast microsatellite markers suggest that the putative somatic hybrids could be L. corniculatus escapes from the asymmetric protoplast fusion process. This thesis details a novel Whole Genome Amplification technique for plants using Strand Displacement Amplification technique.