Evolutionary biology is not a specialty, like genetics or development - it is an explanation of what is investigated by all biological specialties. Thus, the goal of this dissertation was to study both micro- and macroevolutionary processes in a multi-disciplinary framework. Population genetics, conservation, and phylogeny inference. The Jamaican boa (Epicrates subflavus) is an endemic species, whose natural populations greatly and constantly declined since the late 19th century, mainly due to predation by introduced species, human persecution, and habitat destruction. Using species-specific nuclear microsatellite loci and mitochondrial sequences, we investigated the population structure of this endangered reptile. All analyses pinpointed to an Eastern versus (Western+Central) pattern of differentiation in agreement with geological data and patterns of differentiation uncovered in other vertebrate and invertebrate Jamaican species. The same molecular markers were employed on 80 Jamaican boas of the European captive breeding program. This approach allowed us to (i) clarify all ambiguities in the studbook, (ii) correct parental allocation errors and (iii) assess the genetic diversity and the level of inbreeding of the current captive population. These results provide important insights for guiding the development of proper ex-situ and in-situ species survival and habitat management plans for this vulnerable snake. In the same framework of classical evolutionary genetics, we performed preliminary analyses of cytochrome b-like sequences in representatives of all cetacean families (but one), and revealed the presence of at least four nuclear mitochondrial pseudogenes that were independently inserted into the nuclear genome. Evo-Devo. The emergence of Evolutionary Developmental biology has caused a partial shift in the criteria for the selection of model species. Thus far, the main criterion was the relevance of a species for understanding human biology, whereas in the frame of the new discipline, it is the understanding of the generative mechanisms underlying biological diversity that is put forward. We discussed a few criteria and limitations of major relevance to the choice of model species for Evo-Devo studies, and applied a pragmatic approach to identify possible model species within Amniotes. Moreover, we developed MANTiS, an application pipeline that aims at integrating genomic, functional and expression data with evolutionary concepts, thus constituting the missing link between multi-species genome comparisons and functional analyses. Using MANTiS, we proceeded in the analysis of 35 metazoan full genomes for identifying all lineage-specific gene gains and losses. These results were combined with functional and expression analyses, and we demonstrated the much higher performance of MANTiS against popular databases of ortholog clusters (InParanoid, OrthoMCL, RoundUp). Finally, preliminary results of our attempt to adapt the new revolutionary technology of DNA sequencing in microfabricated high-density picoliter reactors (developed by 454/Roche) to the ultra-fast sequencing of brain full transcriptomes in multiple reptilian species are highly promising. As an example, the Crocodylus sample generated more than 72 Mbases (per run), which were successfully assembled in approximately 31,000 contigs. One third of the latter could be matched to known sequences in the transcriptome of related species. After fine-tuning of the in silico analyses, and incorporation of genomic sequence data, we expect our approach to provide important insights not only in the evolution of central nervous system novelties in vertebrates, but in transcriptomes in general as the brain transcriptome is one of the most complex among all organs.

The homeobox superfamily is one of the most significant gene families in the evolution of developmental processes in animals. Within this superfamily the ANTP class has expanded exclusively in animals and, therefore, the reconstruction of its origin and diversification into the different ‘modern' families have become prominent questions in the ‘evo-devo' field. The current burgeoning availability of animal genome sequences is improving the resolution of these questions, putting them in a genome evolution context, as well as providing the field with a large, detailed and diverse catalogue of animal homeobox complements. Here I have contributed with a new hypothesis on the origin and evolution of the Hox and ParaHox loci and the new term, ghost loci, referring to homologous genome regions that have lost their homeobox genes. This hypothesis proposes that the last common ancestor of all animals had a much more complex genome (i.e. differentiated Hox, ParaHox and NK loci) that underwent a simplification in the early animal lineages of sponges and placozoans. In collaboration with the Adamska group I resolved the orthology of the first ever ParaHox genes reported in calcareous sponges. This finding serves as an independent confirmation of the ghost loci hypothesis and further resolves the events of secondary simplification within the sponge lineage. Finally, I have catalogued the homeobox complement of the newly sequenced arthropod, the myriapod Strigamia maritima, and examined the linkage and clustering of these genes. This has furthered our understanding of the evolution of the ANTP class. The diversity of the homeobox complement and the retention in this myriapod and the retention of some homeobox genes not previously described within arthropods, in combination with the interesting phylogenetic position that this lineage occupies relative to other arthropods, makes this complement an important point of reference for comparison within the arthropods and in a broader perspective in the ecdyzosoans. These findings have provided significant further insights into the origin and evolution of the homeobox superfamily, with important implications for animal evolution and the evolution of development.

No description available.

The colonization of the arid continental surface by plants was one of the milestones in Earth's history. Morphological innovations, such as the origin of complex 3D tissues, allowed the successful colonization and radiation of plants on land. The epidermis is the outermost plant tissue that constitutes the interface between the plant and the environment. Thus, the evolution of epidermal cells was crucial for the adaptation of plants on the terrestrial arid environment. I undertook a combined approach that aims to understand the evolutionary trends that drove land plant colonization and the genetic mechanisms that underlie the development of the epidermis. This approach includes: 1) analyses of plant transcription factors (TFs) families distribution and diversification, with a particular focus on the basic Helix-Loop-Helix (bHLH) TF family, and 2) functional characterization of a putatively conserved bHLH TF subfamily involved in epidermal cell development in land plants. Here, I showed that there was a stepwise increase in the number of transcription factor (TF) families and bHLH subfamilies that predated the colonization of the terrestrial surface by plants. The subsequent increase in TF number on land was through duplication within pre-existing TF families and subfamilies. Moreover, a similar trend occurred in metazoan bHLH TF, suggesting that the majority of innovation in plant and metazoan TF families occurred in the Precambrian before the Phanerozoic radiation of land plants and metazoans. Furthermore, I demonstrated that the function of IIIf bHLH TFs in controlling the development of the epidermal cell layer is conserved between liverworts and angiosperms. This suggests that IIIf bHLH TFs are ancient and conserved regulators of epidermal cell development since the early colonization of the land by plants. Moreover, these bHLH TFs were recruited during the evolution of land plants to control the development of seemingly unrelated morphological characters in specific lineages of extant land plants. The recruitment of ancient developmental regulators to control distinct and unrelated developmental processes in land plants might underlie the huge morphological and taxonomic radiation of plants on land.

abstract: This dissertation begins to lay out a small slice of the history of morphological research, and how it has changed, from the late 19th through the close of the 20th century. Investigators using different methods, addressing different questions, holding different assumptions, and coming from different research fields have pursued morphological research programs, i.e. research programs that explore the process of changing form. Subsequently, the way in which investigators have pursued and understood morphology has witnessed significant changes from the 19th century to modern day research. In order to trace this shifting history of morphology, I have selected a particular organ, teeth, and traced a tendril of research on the dentition beginning in the late 19th century and ending at the year 2000. But even focusing on teeth would be impossible; the scope of research on this organ is far too vast. Instead, I narrow this dissertation to investigation of research on a particular problem: explaining mammalian tooth morphology. How researchers have investigated mammalian tooth morphology and what counts as an explanation changed dramatically during this period. / Dissertation/Thesis / Doctoral Dissertation Biology 2017

L'une des caractéristiques les plus frappantes des animaux multicellulaires, aussi appelés les métazoaires, est leur étonnante diversité morphologique. Des études de type phylogénétique ont permis de mettre en relation cette abondance et cette variété observées au sein des formes de vie animale avec des différences au niveau de processus moléculaires, cellulaires, tissulaires et organiques. Parmi ces différences, celle affectant les programmes de développement apparaît comme un aspect clé de la diversité des métazoaires. Les programmes de développement reposent entre autres sur la mise en œuvre de communications entre cellules, ou entre milieu environnant et cellules, et ces communications sont assurées au niveau moléculaire par le déploiement de cascades d'activités protéiques nommées les voies de signalisation. Une des voies de signalisation essentielles au cours du développement de nombreux métazoaires est la voie de l'acide rétinoïque (AR). Le fonctionnement et les rôles de cette voie pendant le développement animal ont fait l'objet de nombreuses recherches, ces travaux ayant aboutis à des découvertes majeures. Néanmoins des analyses supplémentaires restent requises afin de mieux comprendre l'histoire évolutive de cette voie, du métabolisme de l'AR à la transmission de son signal, en passant par l'identification de ses gènes cibles, ses interactions avec d'autres voies de signalisation, et ses fonctions au cours du développement, le tout au sein du règne animal. Dans ce contexte, étudier cette voie chez un métazoaire tel que le céphalochordate amphioxus, qui possède une voie de signalisation de l'AR équivalente à celle des vertébrés, mais avec une redondance moléculaire moindre, représente une étape importante pour identifier l’architecture et les fonctions ancestrales de cette voie parmi les chordés.Chez l’amphioxus, la voie de signalisation de l'AR est étudiée depuis plus de 20 ans, mais peu de choses sont encore connues sur la régulation de la biodisponibilité de l'AR pendant le développement et sur la nature de ses gènes cibles et du réseau régulateur qu’ils définissent. Le but de mon travail de thèse a par conséquent été d’étudier ces deux aspects fondamentaux de la voie de signalisation de l'AR chez l'amphioxus. Au cours de mon projet de recherche, j’ai utilisé comme modèle d’étude l'amphioxus européen, Branchiostoma lanceolatum, pour lequel j’ai également mis en œuvre de nombreuses améliorations du système de culture ainsi que développer des techniques d’analyses in vivo, comme la microinjection d'ARNm dans des œufs. / One of the most striking features of multicellular animals, the metazoans, is their amazing morphological diversity. Even though phylogenetic research has made remarkable progress towards revealing how the abundance and variety of animal life forms relates on the molecular, cellular, tissue, and organismal level, the alteration of developmental programs has been revealed as a key aspect in this process. During development, a rather limited number of signaling pathways has been shown to be instrumental for generating metazoan diversity. The retinoic acid (RA) signaling pathway is one of these instrumental signaling cascades. A significant amount of time and work has been used to characterize the functions and roles of RA signaling during development, although further work is required to better understand the evolutionary history of the RA signaling network, from metabolism to signal transduction passing by the interactions with other signaling cascades and its developmental functions and how they evolve with time. In this context, model organisms with representative, vertebrate-like RA signaling cascades, such as the cephalochordate amphioxus, will be an important case-study in order to identify the blueprint of an ancestral RA network.The amphioxus RA signaling pathway was initially studied about 20 years ago, even though not much is known about the bioavailability of RA during development. Moreover, the target genes of the RA signaling pathway and their hierarchical relationship during amphioxus development represent an interesting open question. Therefore, this work aimed at providing a detailed description of two fundamental aspects of the RA signaling pathway during amphioxus development: (1) the regulation of the bioavailability of RA in the developing embryo and (2) the target genes under the control of the RA signaling pathway together with their hierarchical regulatory relationship. To address these questions, the European amphioxus, Branchiostoma lanceolatum, was used as a model system.During my research project, not only these questions were fundamental, but also the implementation of amphioxus as a reliable model system and thus the establishment of multiple aquaculture improvements as well as in vivo techniques, such as the microinjection of mRNAs into amphioxus eggs. Furthermore, to characterize the bioavailability of RA during development of amphioxus, I focused on the study of the enzymes that mediate the catabolism of RA endogenously, the CYP26 subfamily proteins. I thus described the evolutionary diversification of CYP26 genes in deuterostomes as well as their expression, their function and the mechanisms that govern the feedback loop controlled directly by RA during amphioxus development.Additionally, to shed light on the target genes under the control of the RA signaling pathway during amphioxus development, I combined pharmacological treatments using retinoid-specific drugs with two different techniques of high throughput sequencing: RNAseq, that revealed the entire RNA profile and thus the genes being expressed at a given moment in time, and ATACseq (assay for transposase-accessible chromatin) that provided a global overview of accessible regions of the chromatin (i.e. open chromatin regions). By combining the data obtained by these techniques, I revealed a new set of genes that are under the control of the RA signaling pathway as well as new potential regulatory loops driving RAR-mediated expression. Moreover, I established a framework to characterize gene hierarchies during development that can be widely applied to other signaling pathways and organisms.

Os genes Hox padronizam o corpo dos vertebrados durante o desenvolvimento embrionário, e a compreensão de sua evolução pode elucidar mecanismos genéticos subjacentes à evolução morfológica. A evolução molecular dos genes Hox imprime assinaturas em regiões regulatórias, as quais potencialmente afetam sua expressão gênica, como os elementos cis-regulatórios (CREs) que ladeiam o cluster D de Hox e seus RNAs não-codificantes (ncRNAs). Essa Tese de Doutorado enfoca a evolução regulatória de genes HoxD envolvidos no estabelecimento dos eixos corpóreos axial ântero-posterior (AP) e apendiculares em linhagens de aminiotas que exibem características morfológicas homoplásticas peculiares: os squamatas serpentiformes (Capítulos I e II) e os marsupiais Diprotodontia (Capítulo III). No Capítulo I investigou-se, em serpentes e anfisbênias, se assinaturas regulatórias envolvidas no estabelecimento das morfologias serpentiformes foram impressas na Sequência Conservada B (Conserved Sequence B, CsB), um CRE centromérico de Hoxd10-13. Usando lagartos e outros tetrápodes como referência para a morfologia serpentiforme, regiões conservadas de CsB foram sequenciadas em 38 espécies de Squamata, cujos TFBS foram preditos e comparados. Ambas linhagens serpentiformes exibem assinaturas regulatórias divergentes e convergentes ausentes em lagartos; a convergência localizou-se em um segmento de CsB que concentra perda nas linhagens serpentiformes de diversos TFBS com funções no desenvolvimento de membros e a aquisição de um sítio de ligação para PBX1. Essa assinatura convergente impressa durante evoluções independentes da morfologia serpentiforme pode estar relacionada à elongação corpórea e à perda dos membros, evidenciando um papel do CsB no desenvolvimento do eixo AP. No Capítulo II, foi investigado se um CRE telomérico (CNS65) e um centromérico (Island I) de Hoxd, os quais regulam respectivamente regiões proximais e distais dos membros tetrápodes em desenvolvimento, retêm suas capacidades regulatórias em Serpentes. Expressões de gene repórter desses CREs de serpentes foram realizadas em camundongo transgênico, revelando deficiência de suas atividades regulatórias nos brotos de membro. A comparação dos TFBS preditos nesses elementos entre serpentes e outros tetrápodes revelou que TFBS relacionados ao desenvolvimento dos membros foram perdidos nas sequências das serpentes. Ainda, essa comparação indicou um elemento em CNS65 potencialmente envolvido especificamente na regulação da formação de estilopódio/zeugopódio, e três elementos na Island I exclusivamente reguladores do desenvolvimento autopodial. A perda de membros em x serpentes aparentemente imprimiu assinaturas nesses CREs de Hoxd que possivelmente contribuíram para sua degeneração funcional, putativamente indicando módulos específicos de regulação nos membros. No Capítulo III, ncRNAs do cluster D de Hox foram estudados no contexto da evolução morfológica do autopódio posterior e heterocronia entre o desenvolvimento de membros anteriores e posteriores em Macropus eugenii. Os ncRNAs mapeados sobre o cluster D de Hox foram selecionados a partir de transcritoma de membros de embriões de M. eugenii nos dias 23 (d23) e 25 (d25) de gravidez, e sua conservação, perfis transcricionais e padrões de expressão foram explorados. A comparação com sequências ortólogas de outros mamíferos revelou cinco ncRNAs conservados em mamíferos, e três aparentemente exclusivos dos marsupiais. Os perfis transcricionais de genes HOXD10-13 e dos ncRNAs do cluster D de Hox foram predominantemente equivalentes. Os padrões de expressão de XLOC46 foi similar aos dos genes HOXD terminais de camundongo e M. eugenii, enquanto que XLOC52 e XLOC53 apresentaram expressão idêntica à desses genes em M. eugenii, exceto pela baixa expressão de XLOC53 no d25. Os ncRNAs intergênicos/intrônicos aos genes HOXD9-12 possivelmente regulam a expressão de genes HOXD terminais em mamíferos, enquanto que XLOC52 e XLOC53 constituem bons candidatos para investigação relacionada à evolução dos membros de marsupiais. Esta Tese demonstra como estudos de assinaturas regulatórias na evolução de genes do desenvolvimento contribuem para o entendimento das histórias evolutivas de divergência entre linhagens e d / Hox genes pattern the vertebrate body during embryonic development, and understanding their evolution may unravel genetic mechanisms subjacent to morphological evolution. Molecular evolution of Hox genes entails signatures in regulatory regions that potentially affect gene expression, such as the cis-regulatory elements (CREs) that surround the HoxD cluster and its noncoding RNAs (ncRNAs). In this PhD Thesis, I have explored regulatory evolution of HoxD genes engaged in the development of appendicular and anterior-posterior body (AP) axes in amniotic lineages that exhibit homoplastic morphological peculiarities: snakelike squamates (Chapters I and II) and diprotodontid marsupials (Chapter III). In Chapter I, I investigated in snakes and amphisbaenians, whether equivalent regulatory signatures were registered in the Conserved Sequence B (CsB), a centromeric Hoxd10-13 CRE, during evolution of snakelike morphologies. Using lizards and other tetrapods to represent the lacertiform morphology, conserved regions within CsB were sequenced from 38 squamate species, and transcription factor binding sites (TFBS) were predicted and compared among groups. Both snakelike lineages carry divergent and convergent regulatory signatures not identified in lizards; the convergence located in one CsB segment comprised loss of limb-related TFBS and gain of a binding site for PBX1. This convergent regulatory signature registered along two independent processes of snakelike evolution may relate to body elongation and limb loss, and evidences a role of CsB for AP axis development. In Chapter II, I investigated whether a telomeric (CNS65) and a centromeric (Island I) Hoxd enhancer that regulate gene expression respectively at proximal and distal regions of developing limbs retain their regulatory capacities in Serpentes. Gene reporter expression of these CREs from snakes were performed in transgenic mice and revealed that their regulatory activities were abrogated in limb buds. Comparison of predicted TFBS in these elements between snakes and limbed tetrapods revealed limb-related TFBS apparently lost in snakes, and pointed to one potential stilopodium/zeugopodium-specific element in CNS65 and three likely autopodium-specific elements in Island I. Limb loss in snakes registered signatures in Hoxd CREs that possibly contributed for their functional impairment, putatively indicating limb-specific modules. Finally, in the chapter III, I studied ncRNAs from HoxD cluster in the context of hindlimb morphological evolution and heterochrony between fore and hindlimb development in the tammar wallaby Macropus eugenii. The ncRNAs mapped to HoxD cluster were selected from transcriptome performed using tammar embryo limbs at days 23 (d23) and 25 (d25) of viii pregnancy, and their conservation, transcriptional profiles and expression patterns were explored. Comparison with orthologous sequences in other mammals revealed five ncRNAs conserved among mammals, and three transcripts apparently exclusive to marsupials. Transcriptional profiles of HOXD10-13 and HoxD ncRNAs were mostly equivalent. XLOC46 expression patterns resembled those of mouse and tammar terminal HOXD genes, whereas XLOC52 and XLOC53 showed identical expression patterns to those genes of tammar, except for XLOC53 low expression at d25. The ncRNAs intergenic/intronic to HOXD9-12 may regulate expression of terminal HOXD genes in mammals, and XLOC52 and XLOC53 are suitable for investigation regarding limb evolution in marsupial. This PhD Thesis demonstrates how studies of evolutionary footprints in regulatory elements of developmental genes contribute for elucidating specific processes during lineages divergence as well as functional aspects of these genes during development.

Regeneration, the replacement of lost or damaged body parts, and biomineralisation, the biologically controlled formation of minerals, are important and widespread abilities in the animal kingdom. Both phenomena have a complex evolutionary history; thus their study benefits from investigations in diverse animals. Spirobranchus (formerly Pomatoceros) lamarcki is a small tube-dwelling polychaete worm of the serpulid family. Serpulids have evolved a novel head appendage, the operculum, which functions as a defensive tube plug and regenerates readily when lost. In S. lamarcki, the end of the operculum is reinforced by a calcareous plate; thus, the operculum is a good system in which to study both regeneration and biomineralisation. This thesis explores several aspects of these important processes in the adult operculum. First, a time course of normal regeneration is established. Next, cell proliferation patterns are described, suggesting a combination of proliferation-dependent and proliferation-independent elements in opercular regeneration. The formation of the calcareous opercular plate is examined using both microscopic observations of whole opercular plates and X-ray diffraction analysis of isolated plate mineral, revealing a large shift in mineralogy over the course of regeneration. Histochemical study of alkaline phosphatase enzyme activity indicates the importance of these enzymes in the operculum, although their precise functions are as yet unclear. Finally, a preliminary survey of three opercular transcriptomic datasets is presented, with a broad sampling of gene families with regeneration- or biomineralisation-related roles in other animals. The opercular transcriptome constitutes the first biomineralisation transcriptome from any annelid, and one of the first transcriptomic datasets related to annelid regeneration. Many of the candidate genes examined here display interesting behaviour and suggest targets for further investigation. The work presented here establishes the S. lamarcki operculum as a promising model system in the field of evolutionary developmental biology.

Evolutionary biology is not a specialty, like genetics or development - it is an explanation of what is investigated by all biological specialties. Thus, the goal of this dissertation was to study both micro- and macroevolutionary processes in a multi-disciplinary framework.<p>Population genetics, conservation, and phylogeny inference. The Jamaican boa (Epicrates subflavus) is an endemic species, whose natural populations greatly and constantly declined since the late 19th century, mainly due to predation by introduced species, human persecution, and habitat destruction. Using species-specific nuclear microsatellite loci and mitochondrial sequences, we investigated the population structure of this endangered reptile. All analyses pinpointed to an Eastern versus (Western+Central) pattern of differentiation in agreement with geological data and patterns of differentiation uncovered in other vertebrate and invertebrate Jamaican species. The same molecular markers were employed on 80 Jamaican boas of the European captive breeding program. This approach allowed us to (i) clarify all ambiguities in the studbook, (ii) correct parental allocation errors and (iii) assess the genetic diversity and the level of inbreeding of the current captive population. These results provide important insights for guiding the development of proper ex-situ and in-situ species survival and habitat management plans for this vulnerable snake. In the same framework of classical evolutionary genetics, we performed preliminary analyses of cytochrome b-like sequences in representatives of all cetacean families (but one), and revealed the presence of at least four nuclear mitochondrial pseudogenes that were independently inserted into the nuclear genome. <p>Evo-Devo. The emergence of Evolutionary Developmental biology has caused a partial shift in the criteria for the selection of model species. Thus far, the main criterion was the relevance of a species for understanding human biology, whereas in the frame of the new discipline, it is the understanding of the generative mechanisms underlying biological diversity that is put forward. We discussed a few criteria and limitations of major relevance to the choice of model species for Evo-Devo studies, and applied a pragmatic approach to identify possible model species within Amniotes. <p>Moreover, we developed MANTiS, an application pipeline that aims at integrating genomic, functional and expression data with evolutionary concepts, thus constituting the missing link between multi-species genome comparisons and functional analyses. Using MANTiS, we proceeded in the analysis of 35 metazoan full genomes for identifying all lineage-specific gene gains and losses. These results were combined with functional and expression analyses, and we demonstrated the much higher performance of MANTiS against popular databases of ortholog clusters (InParanoid, OrthoMCL, RoundUp).<p>Finally, preliminary results of our attempt to adapt the new revolutionary technology of DNA sequencing in microfabricated high-density picoliter reactors (developed by 454/Roche) to the ultra-fast sequencing of brain full transcriptomes in multiple reptilian species are highly promising. As an example, the Crocodylus sample generated more than 72 Mbases (per run), which were successfully assembled in approximately 31,000 contigs. One third of the latter could be matched to known sequences in the transcriptome of related species. After fine-tuning of the in silico analyses, and incorporation of genomic sequence data, we expect our approach to provide important insights not only in the evolution of central nervous system novelties in vertebrates, but in transcriptomes in general as the brain transcriptome is one of the most complex among all organs.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Wir fanden konservierte molekulare Signaturen der Regulation durch Δ7-DA und Ascarosid bei Dauer- und infektiösen Larven. Danach wurde die hohe Konservierung durch unsere Analyse in Dauer- und Postdauer-Stadium zwischen den zwei nah verwandten freilebenden Arten C. elegans und C. briggsae identifiziert. Das heißt, dass die relative Veränderung auf mRNA- oder Protein- Ebene zwischen zwei Arten stark korreliert ist. Aber die relative Veränderung innerhalb derselben Art zeigt keine hochgradige Korrelation zwischen mRNA- und Protein-Ebene. Unsere Ergebnisse zeigen in C. elegans Dauerlarven die signifikante Reduzierung der RNA-Mengen in 20 Stoffwechselwegen. Im Gegensatz dazu speicherten Dauerlarven reichlich RNA-Mengen in GO Termen wie Ribosome und Aminoacyl-tRNA biosynthesis. Auf Protein-Ebene sind die Stoffwechselwege von Proteinsynthese und Proteinverarbeitung im endoplasmatischen Retikulum in Dauerlarven herunterreguliert und GO Terme wie Lysosome sind hochreguliert. Durch die Zeitreihenanalyse der Proteom-Remodellierung der molekularen Signaturen beim Austritt aus dem Dauer-Stadium fand wir, dass GO Terme wie metal ion binding signifikant herunterreguliert sind und der Proteinabbau hochreguliert ist. Unsere Ergebnisse vom pSILAC Experiment deuten an, dass die Proteine für Energieerzeugung und Chaperone/Proteinfaltung beim Daueraustritt schnell verbraucht sind und wieder hergestellt werden. Zum Schluss haben wir als Erste den popomR-Assay in C. elegans etabliert und ein Screening der vermeintlichen Proteinbindestellen auf poly-A-RNA durchgeführt, um in der Zukunft die konservierten Mechanismen der post-transkriptionellen Regulation durch RBPs im Dauer-Stadium zu analysieren. / We found the conservation of molecular signatures by regulating with Δ7-DA and Ascarosid in dauer larvae and infective larvae. Then by our comparative analysis, the high degree of conservation between two closely related free-living species C. elegans and C. briggsae was identified in dauer and post-dauer stages. This means that the relative changes are strongly correlated on the mRNA or the protein level between two species. But the relative changes in the same species don’t show any strong correlation between the mRNA and the protein levels. Our results showed a significantly reduced amount of RNA in 20 metabolic pathways in C. elegans dauer larvae. In contrast, dauer larvae stored a large amount of RNA in GO terms such as ribosome and aminoacyl-tRNA biosynthesis. On the protein level, the metabolic pathways of protein synthesis and protein processing in endoplasmic reticulum were downregulated in dauer larvae and the term of lysosome was up-regulated. Due to time course analysis for proteome remodeling of molecular signatures during exit process from dauer stage, we found that GO terms such as metal ion binding were significantly downregulated during dauer exit and at the same time the protein degradation was up-regulated. Our results of pSILAC experiment suggest that the proteins for energy generation and chaperone/protein folding are quickly spent and rebuilded during dauer exit. Finally, we were the first to establish the popomR assay in C. elegans and performed a screening of the putative protein binding sites on poly-A RNA to analyze the conserved mechanisms of post-transcriptional regulation by RBPs in dauer larvae in the future.