Major fraction of eukaryotic genomes is composed of transposons. Mobilization of these transposons leads to mutations and genomic instability. In animals, these selfish genetic elements are regulated by a class of small RNAs called PIWI interacting RNAs (piRNAs). Thus host piRNA pathway acts as a defense against pathogenic transposons. Many piRNA pathway genes are rapidly evolving indicating that they are involved in a host-pathogen arms race. In my thesis, I investigated the nature of this arms race by checking functional consequences of the sequence diversity in piRNA pathway genes. In order to study the functional consequences of the divergence in piRNA pathway genes, we swapped piRNA pathway genes between two sibling Drosophila species, Drosophila melanogaster and Drosophila simulans. We focused on RDC complex, composed of Rhino, Deadlock and Cutoff, which specifies piRNA clusters and regulates transcription from clusters. None of the D. simulans RDC complex proteins function in D. melanogaster. Rhino and Deadlock interact and colocalize in D. simulans and D. melanogaster, but D. simulans Rhino does not bind D. melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain. Cutoff from D. simulans stably binds and traps D. melanogaster Deadlock. Adaptive evolution has thus generated cross-species incompatibilities in the piRNA pathway which may contribute in reproductive isolation.

Cryphonectria parasitica is the causal agent of chestnut blight, which devastated the American Chestnut tree population in the early 20th century. The discovery of hypoviruses that reduce the severity of the chestnut blight infection offers the potential for biological control. However, the spread of the hypoviruses is hampered by a diverse genetically controlled nonself-recognition system, vegetative incompatibility (vic). CPVIB-1 was identified as a transcription regulator playing an important role in the programmed cell death response to this stimulus. In this study, we have found that CPVIB-1 is ubiquitin-decorated which might lead to its degradation in the proteasome pathway. RNA-Seq and ChIP-Seq were used to further explore the downstream targets of CPVIB-1 that mediate the various metabolic changes that lead to the altered phenotype of the Δcpvib-1 mutant. Due to inaccuracies in the prior annotation, we performed a genome re-annotation to improve the accuracy using a MAKER2-two-pass pipeline. To validate the improvement a second pipeline, PEPA, was developed to compare quality metrics between the old and new annotations. Approximately 1/3 of the original annotations from 2009 were found to be inaccurate. Experimental confirmation by testing 27 predicted genes using a diagnostic PCR protocol to differentiate between prior and new transcript structures showed that over 80 % of tested genome locations supported for the new annotation. Using rapamycin treatment to mimic stimulation of the vic response and applying the RNA-seq and ChIP-seq data to this new information, we found that CPVIB-1 is related to TOR signaling pathways, promoting autophagy and the proteasome pathway, but repressing carbon metabolism, protein and lipid biosynthesis. In depth analysis of CPVIB-1-bound DNA targets showed that this protein is a member of the GAGA regulator family, a group of multifaceted transcription factors with diverse roles in gene activation and repression, maintenance of mitosis, and cell development. Following treatment with rapamycin the recognition sequence bound by CPBVIB-1 was altered leading to the regulation of different suite of genes with diverse metabolic functions. Ultimately, we have developed a revised model of TOR signaling pathway where TORC1 and TORC2 signaling pathways are connected by the action of CPVIB1.

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Yes / Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10−5. A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach. / This study was supported by a grant from the Swedish Research Council to T.S.

Conventional fixed base walls are typically characterized by yielding that results in permanent damage, residual drifts and costly losses due to the service shutdown for structural repairs. Controlled rocking masonry walls have been developed as a solution to prevent structural damage when seismic events take place. These systems purposely allow the wall to rock from its foundation and have an uplift at the base, thus replacing the typical yielding at the base of conventional fixed-base walls. Controlled rocking masonry walls have traditionally been controlled by using unbonded post-tensioning strands to provide the self-centering behaviour. Although post-tensioning has shown favourable results, its implementation is difficult in practical applications, and post-tensioning losses due to yielding of the strands at large deformations can reduce their self-centering ability. In order to overcome such issues, an alternative controlled rocking system for masonry walls was developed recently, which is designed to self-center through vertical gravity loads only, instead of the post-tensioning tendons. The rocking response of this alternative system is controlled by using energy dissipation devices, so the system is referred to as Energy Dissipation-Controlled Rocking Masonry Walls (ED-CRMWs). The vertical gravity loads are primarily transferred to the ED-CRMWs from the floor slab at each level. Therefore, the wall-slab interaction should be investigated in order to ensure a fully resilient system. In this regard, the current study identifies and categorizes the potential issues that are expected to occur due to the interaction between the wall rocking mechanism and the floor slab, and then investigates the most common of these issues using a parametric study. The parametric study focuses on the vertical incompatibility of displacements that a hollow- core slab suffers when its supporting walls uplift by different displacements during seismic events. Three different spans, four different cross-sections and two different alternatives of prestress configurations are considered in this study. The models were developed using ABAQUS 6.18 commercial software. The results show the cracking/yielding behaviour of the slabs and their displacement capacities at five different stages. The obtained results are promising for the usage of hollow-core slabs on ED-CRMWs or similar systems that require this interaction, as the range of displacement capacities can accommodate many of the vertical displacement incompatibilities expected in many potential situations. / Thesis / Master of Applied Science (MASc)

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京都大学 / 新制・課程博士 / 博士(工学) / 甲第23889号 / 工博第4976号 / 新制||工||1777(附属図書館) / 京都大学大学院工学研究科原子核工学専攻 / (主査)教授 斉藤 学, 准教授 田﨑 誠司, 教授 宮寺 隆之 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Réalisé au sein de l'IRCAM, en cotutelle avec Philippe Leroux. La version intégrale de cette thèse est disponible uniquement pour consultation individuelle à la Bibliothèque de musique de l’Université de Montréal. / « Vers une musique autogérée », est un regard sur mes œuvres des trois dernières années : un quatuor à cordes, un quatuor pour flûte basse, saxophone baryton, percussion et piano, une pièce pour voix de femme et douze musiciens et une pièce pour silent piano et dispositif électronique, qui sera le chapitre le plus exhaustif. Tout au long de cette étude, on examinera les notions qui m’inspirent, les points de départ de chaque pièce ainsi que les moyens employés pour arriver au bout de chaque idée. On parlera du tandem « intuition – processus » et comment il s’exprime chaque fois de façon différente, des réseaux qui se créent dans la musique, on abordera le concept omniprésent de l’incompatibilité et les relations que cela autorise, et on suivra l’évolution progressive de l’écriture vers une musique qui se veut « autogérée », en examinant comment ce terme se manifeste, selon les différents contextes. / « Towards an autoregulated music » is a look on my works of the past three years: a string quartet, a quartet for bass flute, baritone saxophone, percussion and piano, a work for female voice and twelve musicians and a piece for silent piano and real time electronics, the most thorough chapter. Throughout this study, we’ll examine the notions that inspire me, every piece’s starting points and the means applied to take every idea to its full potential. We’ll talk about the tandem « intuition – process » and how it’s expressed every time in a different way, the networks that exist in the music, we’ll approach the ever-present concept of incompatibility and the relations it allows, and we’ll follow the gradual evolution of the writing towards a music that calls itself « autoregulated », considering how this term is expressed, in different contexts.