No description available.

No description available.

No description available.

No description available.

No description available.

Recurrent processes are a general feature of living systems, from the cell cycle to circadian day-night rhythms to hibernation and flowering cycles. During development and life, numerous recurrent processes are controlled by genetic oscillators, a specific class of genetic regulatory networks that generates oscillations in the level of gene products. A vital mechanism controlled by genetic oscillators is the rhythmic and sequential segmentation of the elongating body axis of vertebrate embryos. During this process, a large collection of coupled genetic oscillators gives rise to spatio-temporal wave patterns of oscillating gene expression at tissue level, forming a dynamic prepattern for the precursors of the vertebrae. While such systems of genetic oscillators have been studied extensively over the past years, many fundamental questions about their collective behavior remain unanswered. In this thesis, we study the behavior and the properties of genetic oscillators from the single oscillator scale to the complex pattern forming system involved in vertebrate segmentation. Genetic oscillators are subject to fluctuations because of the stochastic nature of gene expression. To study the effects of noisy biochemical coupling on genetic oscillators, we propose a theory in which both the internal dynamics of the oscillators as well as the coupling process are inherently stochastic. We find that stochastic coupling of oscillators profoundly affects their precision and synchronization properties, key features for their viability as biological pacemakers. Moreover, stochasticity introduces phenomena not known from deterministic systems, such as stochastic switching between different modes of synchrony. During vertebrate segmentation, genetic oscillators play a key role in establishing a segmental prepattern on tissue scale. We study the spatio-temporal patterns of oscillating gene expression using a continuum theory of coupled phase oscillators. We investigate the effects of different biologically relevant factors such as delayed coupling due to complex signaling processes, local tissue growth, and tissue shortening on pattern formation and segmentation. We find that the decreasing tissue length induces a Doppler effect that contributes to the rate of segment formation in a hitherto unanticipated way. Comparison of our theoretical findings with experimental data reveals the occurrence of such a Doppler effect in vivo. To this end, we develop quantification methods for the spatio-temporal patterns of gene expression in developing zebrafish embryos. On a cellular level, tissues have a discrete structure. To study the interplay of cellular processes like cell division and random cell movement with pattern formation, we go beyond the coarse-grained continuum theories and develop a three-dimensional cell-based model of vertebrate segmentation, in which the dynamics of the segmenting tissue emerges from the collective behavior of individual cells. We show that this model is able to describe tissue formation and segmentation in a self-organized way. It provides the first step of theoretically describing pattern formation and tissue dynamics during vertebrate segmentation in a unified framework involving a three-dimensional tissue with cells as distinct mechanical entities. Finally, we study the synchronization dynamics of generic oscillator systems whose coupling is subject to phase shifts and time delays. Such phase shifts and time delays are induced by complex signaling processes as found, e.g., between genetic oscillators. We show how phase shifts and coupling delays can alter the synchronization dynamics while leaving the collective frequency of the synchronized oscillators invariant. We find that in globally coupled systems, fastest synchronization occurs for non-vanishing coupling delays while in spatially extended systems, fastest synchronization can occur on length scales larger than the coupling range, giving rise to novel synchronization scenarios. Beyond their potential relevance for biological systems, these results have implications for general oscillator systems, e.g., in physics and engineering. In summary, we use discrete and continuous theories of genetic oscillators to study their dynamic behavior, comparing our theoretical results to experimental data where available. We cover a wide range of different topics, contributing to the general understanding of genetic oscillators and synchronization and revealing a hitherto unknown mechanism regulating the timing of embryonic pattern formation.

No description available.

microRNAs (miRNAs), ~21-24 nucleotide-long RNAs that post-transcriptionally regulate gene expression, have rapidly become one of the most extensively studied mechanisms of the past decade. Since their discovery as temporal regulators of post-embryonic development in C. elegans, miRNAs have been functionally implicated in almost every cellular process investigated to date. miRNAs are integral to the complex biological processes of embryonic development and aging. In this research, we sought to determine whether misregulation of miRNAs could be responsible for eliciting adverse effects during these two distinct developmental stages. First, to uncover the potential role of miRNAs in teratogenicity, we investigated whether miRNAs were involved in regulation of retinoic acid (RA) induced vertebrate axis defects. Global miRNA expression profiling revealed that RA exposure suppressed the expression of miR-19 family members during zebrafish somitogenesis. Bioinformatics analyses predict that miR-19 targets cyp26a1, a key RA detoxifying enzyme, and a physiological reporter assay confirmed that cyp26a1 is a bona fide target of miR-19. Transient knockdown of miR-19 phenocopied RA-induced body axis defects. In gain-of-function studies, exogenous miR-19 rescued the axis defects caused by RA exposure. Our findings indicate that the teratogenic effects of RA exposure result, in part, from repression of miR-19 and the subsequent misregulation of cyp26a1. This highlights a previously unidentified role of miR-19 in facilitating vertebrate axis development. Next, to explore whether age-related changes in miRNAs trigger deficits in regeneration capacity, we performed mRNA and small RNA sequencing on regenerating and non-regenerating caudal fin tissue from aged, adult and juvenile zebrafish. An unbiased approach identified cbx7 as the most abundant transcript with significantly increased expression in regenerative-competent adult and juvenile tissue and decreased expression in regenerative-compromised aged tissue. While cbx7 is a known regulator of aging, this is the first report of its role in tissue regeneration. A computational approach was used to discover mRNAs expressed during regeneration, which are potential targets of the significantly expressed miRNAs in regenerating tissue. miR-21 was one of the most abundant and significantly increased miRNAs in regenerating tissue and exhibited an aberrant age-dependent expression profile. Bioinformatics predicts miR-21 to target the 3' UTR of cbx7 and a reporter assay confirmed that miR-21 targets cbx7 in vivo. Transient knockdown of miR-21 inhibited tissue regeneration, suggesting a role for miRNA mediated regulation of cbx7 during regeneration. These findings reveal a novel, age-dependent regenerative function of cbx7 and emphasize the importance of miR-21 as a master regulator of vertebrate regenerative responses. This research, when combined, underscores the negative consequences misregulation of miRNAs has on embryonic development and aging. / Graduation date: 2013 / Access restricted to the OSU Community at author's request from Dec. 5, 2012 - Dec. 5, 2013

La segmentation de l’axe antéro-postérieur en somites est une caractéristique majeure des Vertébrés. Ce processus est basé sur un oscillateur, l’« horloge de segmentation ». Cette thèse cherche à comprendre la dynamique de signalisation régulant ce processus. Nous avons étudié la régulation transcriptionnelle de Mesp2 et nous avons montré que Tbx6 contrôle son expression chez le poulet. Nous présentons également un système d’étude ex vivo présentant des oscillations stables du gène cyclique Lfng. Nous avons mis en évidence un effet de population régulant la génération de ces oscillations et reposant sur la voie Notch et des facteurs mécaniques que nous interprétons avec un modèle d’oscillateur excitable. De plus, nous avons démontré un effet dose-dépendant de la voie Fgf sur la différenciation cellulaire, remettant ainsi en question le modèle actuel de segmentation. Par ailleurs, ce système d’étude nous a permis d’identifier un rôle du taux de traduction dans le contrôle de la période de l’horloge. Enfin, nous présentons des travaux, où nous cherchons à reconstituer l’horloge de segmentation in vitro à partir de cellules souches murines différenciées. / The segmentation of the anteroposterior axis in somites is a major feature of Vertebrates. This process relies on an oscillator, the “segmentation clock”. The present thesis addresses the signaling dynamics regulating this process. We studied the transcriptional regulation of Mesp2 and showed that Tbx6 controls its expression in chicken. We established an ex vivo experimental system with stable oscillations of the cyclic gene Lfng. We demonstrated the existence of a population behavior that controls the generation of oscillations and involves the Notch pathway and mechanical factors. We interpreted these observations in the framework of an excitable oscillator. Moreover, we evidenced a dose-dependent effect of Fgf signaling on cell determination that challenges current models of segmentation. Furthermore, this experimental system has enabled us to identify a role of the translation rate on the clock period. Last, we showed ongoing work aiming to recapitulate the segmentation in vitro using differentiated mouse embryonic stem cells.

Recurrent processes are a general feature of living systems, from the cell cycle to circadian day-night rhythms to hibernation and flowering cycles. During development and life, numerous recurrent processes are controlled by genetic oscillators, a specific class of genetic regulatory networks that generates oscillations in the level of gene products. A vital mechanism controlled by genetic oscillators is the rhythmic and sequential segmentation of the elongating body axis of vertebrate embryos. During this process, a large collection of coupled genetic oscillators gives rise to spatio-temporal wave patterns of oscillating gene expression at tissue level, forming a dynamic prepattern for the precursors of the vertebrae. While such systems of genetic oscillators have been studied extensively over the past years, many fundamental questions about their collective behavior remain unanswered. In this thesis, we study the behavior and the properties of genetic oscillators from the single oscillator scale to the complex pattern forming system involved in vertebrate segmentation. Genetic oscillators are subject to fluctuations because of the stochastic nature of gene expression. To study the effects of noisy biochemical coupling on genetic oscillators, we propose a theory in which both the internal dynamics of the oscillators as well as the coupling process are inherently stochastic. We find that stochastic coupling of oscillators profoundly affects their precision and synchronization properties, key features for their viability as biological pacemakers. Moreover, stochasticity introduces phenomena not known from deterministic systems, such as stochastic switching between different modes of synchrony. During vertebrate segmentation, genetic oscillators play a key role in establishing a segmental prepattern on tissue scale. We study the spatio-temporal patterns of oscillating gene expression using a continuum theory of coupled phase oscillators. We investigate the effects of different biologically relevant factors such as delayed coupling due to complex signaling processes, local tissue growth, and tissue shortening on pattern formation and segmentation. We find that the decreasing tissue length induces a Doppler effect that contributes to the rate of segment formation in a hitherto unanticipated way. Comparison of our theoretical findings with experimental data reveals the occurrence of such a Doppler effect in vivo. To this end, we develop quantification methods for the spatio-temporal patterns of gene expression in developing zebrafish embryos. On a cellular level, tissues have a discrete structure. To study the interplay of cellular processes like cell division and random cell movement with pattern formation, we go beyond the coarse-grained continuum theories and develop a three-dimensional cell-based model of vertebrate segmentation, in which the dynamics of the segmenting tissue emerges from the collective behavior of individual cells. We show that this model is able to describe tissue formation and segmentation in a self-organized way. It provides the first step of theoretically describing pattern formation and tissue dynamics during vertebrate segmentation in a unified framework involving a three-dimensional tissue with cells as distinct mechanical entities. Finally, we study the synchronization dynamics of generic oscillator systems whose coupling is subject to phase shifts and time delays. Such phase shifts and time delays are induced by complex signaling processes as found, e.g., between genetic oscillators. We show how phase shifts and coupling delays can alter the synchronization dynamics while leaving the collective frequency of the synchronized oscillators invariant. We find that in globally coupled systems, fastest synchronization occurs for non-vanishing coupling delays while in spatially extended systems, fastest synchronization can occur on length scales larger than the coupling range, giving rise to novel synchronization scenarios. Beyond their potential relevance for biological systems, these results have implications for general oscillator systems, e.g., in physics and engineering. In summary, we use discrete and continuous theories of genetic oscillators to study their dynamic behavior, comparing our theoretical results to experimental data where available. We cover a wide range of different topics, contributing to the general understanding of genetic oscillators and synchronization and revealing a hitherto unknown mechanism regulating the timing of embryonic pattern formation.