The maintenance of genomic stability through suppression of retrotransposon activity is vital for the avoidance of potentially mutagenic genomic disruption caused by retrotransposition. Germline development is a particularly important phase for retrotransposon silencing as retrotransposition events here have the potential for transmission to the entire embryo, threatening the health of offspring. A collection of germline genome defence genes are required for the suppression of retrotransposons in the developing germline of male mice (e.g. Tex19.1, Dazl, Mili, Miwi2, Gasz, Mov10l1, Mael, Dnmt3l), all of which trigger meiotic prophase arrest when mutated. I have analysed the meiotic defects which arise in Tex19.1-/- male mice to contribute to the understanding of the fundamental mechanisms required for successful completion of meiosis and to investigate the involvement of retrotransposon silencing in this process. The absence of TEX19.1 in male mice causes infertility; with failed chromosome synapsis in ~50% of pachytene nuclei and associated apoptosis, as well as individual univalent chromosomes in 67% of remaining nuclei progressing to metaphase I. Where studied, failed chromosome synapsis is a common feature of germline genome defence mutant spermatocytes. One aim of my studies has been to better understand the mechanism responsible for this failed chromosome synapsis. I have demonstrated that unlike Mael-/- spermatocytes, additional SPO11-independent DNA damage potentially attributable to retrotransposition is not detectable in Tex19.1-/- spermatocytes. Rather, the formation of meiotic DNA double strand breaks (DSBs) is dramatically reduced in early prophase to around 50%, resulting in a reduction in nuclear γH2AX signal, production of SPO11- oligonucleotide complexes and foci formation by early recombination proteins RPA, DMC1 and RAD51. Despite this early reduction, DSB frequency recovers to more normal levels shortly after in zygotene. I have shown that defective pairing of homologous chromosomes by meiotic recombination is likely responsible for the asynapsis previously reported. The initial reduction in DSB frequency could be sufficient to cause failed chromosome synapsis in this mutant, assuming that late-forming DSBs cannot participate effectively in promoting homologous pairing. Alternative hypotheses include altered positioning of DSBs in response to altered chromatin organisation relating to retrotransposon upregulation, misguiding the pairing of homologous chromosomes. Such a model of disruption could also extend to other germline genome defence mutants. I have demonstrated that despite successful pairing of homologous chromosomes in a sub-population of Tex19.1-/- spermatocytes, subsequent progression of these cells through pachytene is delayed. Numerous diverse features of progression are all delayed, including recombination, ubiquitination on autosomes and sex chromosomes, expression of the mid-pachytene marker H1t, and chromosome organisation. The delay identified is related to recombination therefore this feature is likely to stem from the initial defect in DSB formation early in prophase. While some delayed features are probably directly related to recombination, others are not. The coordinated delay observed may suggest the presence of a recombination-sensitive cell-cycle checkpoint operating to regulate progression through pachytene. My research has also aimed to establish the cause of elevated univalent chromosomes not connected by chiasmata in metaphase I Tex19.1-/- spermatocytes. I have demonstrated that that absence of chiasmata is not due to failed crossover formation between synapsed chromosomes. Rather, the frequent observation of individual unsynapsed chromosomes during crossover formation suggests that some spermatocytes with low-level asynapsis are leaking through meiotic checkpoints and are unable to form a crossover before reaching metaphase. Therefore, again this later meiotic defect appears to stem from the initial defect in meiotic DSB formation, the consequences of which vary widely in severity. Remarkably the unsynapsed chromosomes present during crossover formation include both sex chromosomes, and autosomes. Tolerance of an unsynapsed autosome from pachytene into metaphase is an unusual observation in mice and this observation may aid the understanding of spermato cyte quality control mechanisms during this progression. Together these findings have greatly advanced the understanding of the infertility incurred during meiosis in Tex19.1-/- male mice. These findings may also extend to benefit the understanding of other germline genome defence mutants. Diverse observations made during my investigations also reveal a potential system of coordinated progression through pachytene relating to meiotic recombination. The variable severity of the synapsis defects incurred in this mutant appears to have variable effects on spermatocyte survival and could also inform the understanding of meiotic checkpoint sensitivity.

Easy manufacturing, light weight and inexpensive materials are the key qualities of organic solar cells that makes them a highly researched area. To make organic solar cells adequate for the market, the efficiency of power conversion has to increase further, and the lifetime of organic solar cells has to improve. Avoiding recombination losses is a piece in the puzzle that can make organic solar cells more efficient. Organic solar cells with two different hole transport layers were therefore examined by I-V measurements. It was found that the organic solar cell with MoO3 as the HTL possesses a higher current density in both the reverse region and forward region. The higher current density in both regions points towards a less successful blocking of electrons travelling to the anode (reverse region) and a better ability to transport holes from the active layer to the anode. Insight to different state of recombination was also found from the slope values in the Voc and Jsc as a function of light intensity plots. It was concluded that both solar cells experience a dominant monomolecular recombination under short circuit condition and evolved into bimolecular recombination under open circuit condition. However, the cell with CuSCN showed a more dominant bimolecular recombination, which was shown from a slope closer to one unity kT/q in the Voc as a function of light intensity plot.

Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species.

Meiotic recombination, known as crossover, is a vital mechanism for generating genetic diversity in sexually reproducing populations. Recombination events are non-uniform across the genome, due to a variety of influences including chromatin structure, DNA-sequence, epigenetic marks and interference from other recombination events. These known factors do not fully explain the distribution of recombination events, and additionally do not account for all the variability in recombination frequency observed both between and within species. Furthermore, of the mechanisms that have been identified, many are not yet fully understood. In Arabidopsis thaliana, considerable variation is observed in recombination frequency and distribution between natural accessions. By investigating recombination events in A.thaliana, this project aimed to identify trans-acting modifiers of recombination frequency that varied between natural accessions. Identification of meiotic recombination modifiers was performed through Quantitative Trait Loci (QTL) mapping in A.thaliana natural-accession cross populations. Populations were generated from crosses between two accessions which differed significantly for recombination frequency as measured across a defined region of the genome flanked by a fluorescent-reporter system. F1 plants were then self-fertilised to produce segregating mosaic F2 populations for mapping. Recombination frequency for specific genomic intervals was determined for each individual in the population through measurement of the segregation of flanking fluorescence-genes expressed in the products of meiosis - seeds or pollen. Individuals were also genotyped using accession-specific markers across the genome, at a marker density of one marker per 2-5Mb, depending on the chromosome. Association of variation in recombination frequency with specific sections of the genome differing between the parental accessions through QTL mapping revealed significant modifiers of meiotic recombination segregating within the populations. This resulted in the identification of three significant large-effect modifiers that differed between Col-0 and Cvi-0 accessions, on chromosomes 1 ,2 and 5, affecting recombination in an interval in the sub-telomere region of chromosome 3. An additional modifier on chromosome 4 affecting the same sub-telomeric interval was identified that differed between the Col-0 and Can-0 accessions. Further fine-mapping of modifiers to improve location resolution was performed by repeated backcrosses into the Col-0 genetic background to remove the influence of other large-effect QTL and possible unknown small-effect modifiers. Improving the resolution provided a number of potential candidates for genes underlying the recombination phenotype for each QTL. Candidate testing was then performed, either through transformation of different accession alleles into the fluorescent-reporter system, or through analysis of T-DNA insertion lines that interrupted candidate genes. Preliminary results from T-DNA insertion mutants crossed to the fluorescent-reporter system suggest a potential role for the AT2G31510 gene in modification of meiotic recombination frequency, though the mode of action remains unknown. These results demonstrate the presence of large-effect modifiers of meiotic recombination frequency that vary between the natural A.thaliana accessions Col-0, Cvi-0 and Can-0. Confirmation of underlying genes or sequence elements and characterisation of their mechanism of action are opportunities for exploration in future experiments.

Manipulation de la recombinaison chez une plante cultivée, le riz.L’accroissement prévisible de la population mondiale ainsi que les conséquences du changement climatique obligent les sélectionneurs à créer de nouvelles variétés plus productives et plus résilientes. Les nouvelles combinaisons d’allèles favorables sont issues de la recombinaison génétique entre chromosomes homologues dont le siège est la prophase de première division de méiose. De récentes avancées chez la plante modèle Arabidopsis ont montré que l'inactivation de certains gènes permet de manipuler la méiose pour abolir ou au contraire augmenter très significativement la recombinaison. Les mécanismes de la méiose étant relativement bien conservés chez les eucaryotes, l’objectif de cette thèse était de transposer ces avancées chez une plante cultivée importante, le riz. Abolir la recombinaison méiotique permettrait de propager de façon clonale par grain des formules variétales hybrides F1 dont le rendement est de 20% supérieur à celui des lignées pures chez le riz mais dont les semences restent peu utilisées par les riziculteurs de subsistance. Les travaux réalisés dans une première partie de la thèse ont montré que le cumul de trois mutations Ososd1, pair1 et Osrec8, permettait d’obtenir des gamètes clonaux diploïdes mâles et femelles. Le phénotype apoméiotique obtenu, appelé MiMe (Mitosis instead of meiosis) chez Arabidopsis, peut être utilisé pour tester différentes stratégies d’induction de la parthénogenèse afin de produire des grains formant des plantes diploïdes clonales apomictiques. Une optimisation du mécanisme permettrait d'envisager l'utilisation de l'apomixie pour fixer l'hétérosis dans les semences hybrides F1. Par ailleurs, une augmentation globale ou locale de la recombinaison méiotique est recherchée car elle permettrait de diminuer la taille des populations de sélection et de réduire la taille des segments chromosomiques introduits dans les variétés élite de riz. Nous avons montré dans une seconde partie, que la mutation du gène OsRECQl4 codant pour une hélicase permet d'augmenter le taux de recombinaison d'un facteur de 3,3 fois faisant passer la taille de la carte génétique de 1670 cM à 5538 cM sans affecter la fertilité de la plante ni le déroulement de la méiose. Chez les plantes affectées dans la fonction d’une autre hélicase, OsFANCM, le taux de recombinaison a été également augmenté mais dans une moindre mesure (x 2,2). L’augmentation de la recombinaison s’opère sur l'ensemble des bras chromosomiques sauf au niveau des centromères. Ces résultats confirment ceux obtenus chez A. thaliana qui ont montré le rôle de régulateur négatif des crossing-overs (CO) des protéines RECQ4 et FANCM. La combinaison en cours de ces mutations entre elles ou avec celle affectant l’AAA-ATPase FIGL1 permet d’espérer une augmentation de la recombinaison encore supérieure. Ces résultats ouvrent la voie à l'utilisation des gènes anti-COs pour augmenter de façon globale le nombre de recombinants dans les croisements chez le riz et sans doute chez les autres céréales. Pour offrir une possibilité concrète aux sélectionneurs d'utiliser les gènes anti-CO, nous avons montré que la technologie CRISPR/cas9 permet d'éteindre l'expression de OsFANCM OsRECQl4 et OsFIGL1. / Manipulation of recombination in a crop, rice.The forecasted increase of world population as well as the consequences of global climate change oblige plant breeders to develop new varieties that are both more productive and resilient. Novel combinations of favourable alleles are generated through genetic recombination between homologous chromosomes, which occurs during the prophase of the first division of meiosis. Recent advances in the model plant Arabidopsis have demonstrated that the inactivation of some genes allows meiosis manipulation resulting in either an abolishment or in contrast, a significant enhancement of meiotic recombination. The meiosis mechanisms being relatively conserved across eucaryotes, the overall objective of this thesis was to transfer these advances to a crop of crucial importance, rice. To abolish meiotic recombination would allow the clonal propagation by seeds of F hybrids, which exhibit a 20% yield enhancement compared to that of pure lines in rice but remain rarely used in subsistence farming. In a first part, we showed that rice plants cumulating 3 mutations inactivating Ososd1, pair1 and Osrec8, formed clonal diploid male and female gametes. This apomeiotic phenotype, called MiMe (Mitosis instead of meiosis) in Arabidopsis, can serve as material to assay several strategies of parthenogenetic induction that would result in seed forming diploid clonal plants. Further optimization of the mechanisms would allow the use of apomixis to fix heterosis in hybrid seeds. Global and local enhancement of recombination is another desirable goal since it would allow a reduction in breeding population size and a downsizing of the introgressed chromosomal segments in elite plant materials. In a second part, we showed that mutation in the DNA helicase gene OsRECQl4 conducted to a 3.3 fold increase of recombination and inflated the genetic map size from de 1670 cM to 5538 cM, without altering plant fertility nor meiosis progression. Plants altered in a second DNA helicase, OsFANCM, exhibited a more modest 2.2 fold recombination enhancement. Recombination increase operated along the whole chromosome arms except at the centromere level. These results confirms the negative regulator role of RECQ4 and FANCM on crossing overs (CO), previously reported in Arabidopsis. On going combination of these mutations together with that altering the l’AAA-ATPase FIGL1 should conduct to an even higher recombination enhancement. These results pave the way to the use of anti-CO genes to enhance recombinant recovery in crosses of rice and possibly of other cereals. To provide breeders with a workable anti-CO system, we eventually showed that the CRISPR/Cas9 technology can be used to abolish OsFANCM, OsRECQl4 and OsFIGL1 expression.

Made available in DSpace on 2014-10-09T12:33:11Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:06:13Z (GMT). No. of bitstreams: 0 / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Made available in DSpace on 2014-10-09T12:54:50Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:06:59Z (GMT). No. of bitstreams: 0 / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energéticas e Nucleares - IPEN/CNEN-SP

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La recombinaison méiotique n'est pas distribué de manière aléatoire le long des chromosomes, mais est caractérisée par des domaines froids et chauds qui limitent la diversité génétique transmise par les gamètes. Cependant, le profil de la recombinaison méiotique peut être modifiée, étant donné que la fusion de l’ endonucléase Spo11 au domaine de liaison à l'ADN de Gal4 est suffisante pour favoriser la formation des cassures double brin (CDB) et la recombinaison à proximité des sites de liaison de Gal4, dans la levure et dans les souris. Ici, dans la levure Saccharomyces cerevisiae, nous avons étudié l'effet de la fusion de Spo11 à 8 protéines de liaison à l'ADN lors de la méiose. Comme modules de ciblage, nous avons utilisé des facteurs de transcription de levure et des protéines artificiels de liaison à l'ADN (TALEs et ZFs), qui sont apparus comme des outils efficaces pour faire varier la position et / ou le nombre de sites ciblés. Lors de l'expression de chacun des fusions Spo11, nous avons examiné la progression de la méiose, la formation des CDB dans les sites naturels et ciblées ainsi que le niveau relatif de la recombinaison méiotique. Ce travail dans l’organisme modèle levure ouvre de nouvelles voies pour modifier la recombinaison méiotique chez d'autres organismes, tels que des mammifères et des plantes, pour augmenter la diversité génétique dans les sites d'intérêt et disséquer l'information génétique, en surmontant les limitations dues à la liaison génétique. / Meiotic recombination is not randomly distributed along the chromosomes, but is characterized by hot and cold domains that limit the genetic diversity transmitted by the gametes. However, the recombination profile can be modified, since the tethering of Spo11 endonuclease, upon fusion to the Gal4 DNA-binding domain, is sufficient to enhance DSB formation and recombination near several Gal4 consensus binding sites, in yeast and in mouse. Here, in the yeast Saccharomyces cerevisiae, we studied the effect of Spo11 fusions to 8 different DNA-binding proteins during meiosis. As targeting modules, we used yeast full-length transcription factors and artificial DNA-binding modules (TALEs and ZFs), which emerged to be efficient tools to vary the location and /or the number of targeted sites. Upon expression of each of the Spo11 fusions, we examined meiotic progression, DSB formation at natural and targeted sites as well as the relative level of meiotic recombination. This work in the yeast model opens new avenues to modify meiotic recombination in other organisms, such as mammals and plants, to boost genetic diversity at sites of interest and to dissect the genetic information, overcoming the restrictions due to the genetic linkage.

Made available in DSpace on 2014-10-09T12:54:50Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:06:59Z (GMT). No. of bitstreams: 0 / Ímãs sinterizados foram produzidos utilizando o pó obtido pelo processo de Hidrogenação, Desproporção, Dessorção e Recombinação (Processo HDDR). O processo HDDR na produção de ímãs sinterizados foi adotado visando uma redução no tempo de moagem e investigar seu efeito nas propriedades magnéticas e na microestrutura. As ligas utilizadas nesse trabalho apresentaram a seguinte composição: Pr14FebalCoxB6Nb0,1 (x= 0; 4; 8; 10; 12; 16) e Pr20,5Fe72,5B5Cu2,0 (utilizada como aditivo de sinterização). O pó HDDR foi utilizado para produzir ímãs sinterizados com uma mistura dessas ligas (liga principal + aditivo), nas seguintes proporções: 80 % em peso da liga principal e 20% em peso do aditivo de sinterização (Pr20,5Fe72,5B5Cu2,0). O processo de decrepitação por hidrogênio (Processo HD) na produção de ímãs também foi utilizado nesse trabalho para efeito de comparação (tempos de moagem: 20, 15, 10 e 5 horas). A temperatura e o tempo de sinterização foram mantidos constantes para todos os ímãs (1050 º C por 60 minutos). O ímã sinterizado produzido pelo processo HD apresentou melhor remanência (1220 mT).Esse ímã foi fabricado com a liga Pr14Fe75,9B6Co4Nb0,1 utilizando um tempo de 20 horas de moagem. A melhor coercividade intrínseca foi obtida com a liga Pr14Fe75,9B6Co4Nb0,1 em ambos os processos, de 1020 mT para o processo D (5 horas de moagem) e de 1190 mT para o processo HD (20 horas de moagem). As microestruturas dos ímãs permanentes foram analisadas por microscopia eletrônica de varredura (MEV) e por dispersão de energia de raios-X (EDS). / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energéticas e Nucleares - IPEN/CNEN-SP