Relógios endógenos controlam grande parte de processos biológicos através de osciladores bioquímicos que coordenam a sinalização de pistas ambientais até vias metabólicas, permitindo a percepção do tempo e adaptação a mudanças rítmicas. Comportamentos cíclicos diários foram primordialmente descritos em plantas e, mais recentemente, têm fornecido informações valiosas sobre os ciclos de retroalimentação da transcrição e tradução de genes que controlam estes osciladores. O florescimento é um exemplo bem conhecido da importância da percepção do comprimento do dia através do relógio, processo intimamente regulado por fotorreceptores e pelos genes centrais e periféricos do relógio biológico. Em organismos multicelulares há uma combinação específica de genes mais expressa em cada tecido, podendo ter funções, fases e períodos diferentes, o que aumenta a complexidade desse mecanismo. Devido a isso, tem-se buscado modelos alternativos mais simples dentro dos eucariotos fotossintetizantes relacionados às plantas terrestres. Modelos simplificados facilitam, por exemplo, a avaliação da combinação de fatores que induzem o estresse e como o relógio biológico se altera, permitindo a antecipação de mudanças ambientais e sincronização da fisiologia com o meio ambiente. Neste trabalho, verificou-se como o relógio circadiano se ajusta ao estresse em 3 diferentes modelos: Gracilaria tenuistipitata (Rhodophyta), Ostreococcus tauri (Chlorophyta) e Saccharum sp (Embryophyta). Para isso, estabeleceu-se em G. tenuistipitata métodos para avaliação de crescimento e da fluorescência da clorofila de modo automático, comprovando da existência de ritmos circadianos. Além disso, após padronização de genes de referência para normalização das RT-qPCRs, o gene TRX ficou superexpresso durante a primeira hora após o déficit hídrico. Já em O. tauri, onde os genes centrais do relógio são conhecidos, mudanças na expressão de LOV-HK e TOC1 estão relacionadas com maior crescimento em baixa e alta temperatura, respectivamente. Uma combinação específica de luz, temperatura e salinidade pode ser um importante indutor de eflorescências que reflete mudanças transcricionais no oscilador central, o que pode ser comparado às florescências de plantas terrestres. Já em Saccharum sp tolerante à seca, ritmos de fotossíntese e de expressão de CCA1 sofrem mudanças de fase em suas oscilações e transcritos de HVA-22 e DRP são significativamente mais expressos sob dessecação. Em suma, o estresse em Saccharum sp reseta o relógio, aumentando o período de oscilação da fotossíntese. Em O. tauri induz maior crescimento, mantendo as características do relógio. Não foi possível avaliar o efeito do estresse no relógio de G. tenuistipitata, mas ferramentas foram desenvolvidas visando este objetivo. Estudos de respostas do relógio podem fornecer informações valiosas para o entendimento da reprodução e crescimento de organismos com elevado potencial de aplicações biotecnológicas. / Endogenous clocks control a large range of biological processes through biochemical oscillators that coordinate the signaling of environmental cues to metabolic pathways, allowing the perception of time and adjust to rhythmic changes. Cyclical daily behaviors were first noticed in plants and, more recently, revealed information about the transcriptional-translational feedback loops of genes that control these oscillators. Flowering is a well-known process where the perception of day length by the clock is intimately regulated by photoreceptors and by the central and peripheric genes of the biological clock. Multicellular organisms have a tissue-specific combination of expressed clock genes that may have different phase and period, increasing the complexity of this mechanism. Due to this reason, alternative models have been proposed for land plants-related photosynthetic eukaryotes. New models can simplify, for example, which combination of factors induce stress and how the biological clock is altered, allowing the anticipation of environmental changes and synchronization of physiology and environmental factors. This work aimed to verify how the biological clock adjusts to different kinds of stresses in 3 species: Gracilaria tenuistipitata (Rhodophyta), Ostreococcus tauri (Chlorophyta) and Saccharum sp (Embryophyta). Automated measurement techniques for growth rate and photosynthesis were stablished for the red alga. This alga also showed, after establishment of reference genes for RT-qPCRs normalization, an overexpression of TRX during the first hour under water deficit. In O. tauri, where the central clock genes are known, changes in LOV-HK and TOC1 gene expression are related to a higher growth rate under low and high temperatures, respectively. Besides, a specific combination of light, temperature and salinity can be an important trigger of seasonal blooms that causes important transcriptional changes at the central oscillator, what is similar to land plants. In Saccharum sp tolerant to drought, photosynthesis rhythms and CCA1 expression change their phase under simulated water deficit and drought responsive transcripts like HVA-22 and DRP are significantly up-regulated. In short, stress resets the clock in Saccharum sp, increasing the period of photosynthesis oscillation. In O.tauri, it induces a higher growth, keeping clock features. It was not possible to verify clock responses to stress in G.tenuistipitata, but methods to do so were stablished. The biological clock responses to stress can provide invaluable information for the better understanding about the growth and reproduction of organisms with a high biotechnological potential

The circadian clock defines physiologically optimal times for sleeping, which vary along a continuum of circadian phenotypes from morning- to evening-type. Although different ‘chronotypes’ can be discriminated reliably by the Morningness/Eveningness Questionnaire (MEQ), there is little published information on their prevalence. The timing of sleep is also heavily influenced by societal norms. However, the relative contribution of circadian physiology versus psychosocial factors is unknown. This thesis took a multidimensional approach to investigating preferred sleep timing within the general population of New Zealand (30-49 years). A New Zealand version of the MEQ was mailed to a random stratified sample of 5,000 adults living in the Wellington region (55.7% response rate). Using scoring criteria for middle-aged adults, approximately 25% of the population were morning-types and 25% were evening-types. The sleeping patterns of 15 morning- and 16 evening-types were monitored using actiwatches and sleep diaries. Morning-types slept significantly earlier, but there were no differences in sleep duration or quality. Both chronotypes showed evidence of using the weekend to catch-up on sleep, although this was more evident among evening-types. Differences between chronotypes were also investigated using the endogenous melatonin rhythm as a circadian phase marker. The timing of the melatonin rhythm was earlier among morning-types, with the difference being greater for melatonin onset, than offset. However, differences between weekday versus weekend sleep explained more of the variability in sleep timing that did circadian phase. Understanding the genetic differences in the circadian clock is evolving rapidly. While this is of particular scientific interest, little consideration has been given to the ethical implications of this type of work. In the final study, a Kaupapa Māori framework was used to explore Māori hopes and concerns for genetic research in Aotearoa/New Zealand. Thematic analysis indicated that Māori are not anti-science, however there is an urgent need for ethical guidelines that uphold and respect the values of Māori society. This thesis argues that sleep is a major public health issue for New Zealand. However, a number of challenges must be met to ensure that new scientific knowledge meets the needs and expectations of the community.

Circadian oscillators or clocks are a widespread, endogenous class of oscillatory mechanisms that control the ~24h temporal pattern of diverse organism functions. In cyanobacteria this mechanism is formed by three proteins, KaiA, KaiB and KaiC. KaiA is shown here to be a two domain protein that directly interacts with KaiC and enhances the KaiC autokinase activity. The amino-terminal domain of KaiA can be structurally categorized as a pseudo-receiver, a class of proteins used in signaling cascades and activated by direct protein??protein interactions. The carboxy-terminal domain interacts directly with KaiC, is sufficient to enhance the KaiC autokinase activity in a manner similar to full-length KaiA, and adopts a unique, all α-helical dimeric fold. The structure of this domain raises interesting probabilities regarding the mode of KaiA??KaiC interaction. The two KaiA domains are shown to directly interact with each other, which suggests a possible mechanism of signal transfer from the amino to carboxy-terminal domain. Hydrogen bonds are of paramount importance in nucleic acid structure and function. Here we show that changes in the width and anharmonicity of vibrational potential energy wells of hydrogen bonded groups can be measured in nucleic acids and can possibly be correlated to structural properties, such as length. Deuterium/protium fractionation factors, which are sensitive to the vibrational potential well width, were measured for the imino sites of thymidine residues involved in A:T base pairs or free in solution, and a correlation was established between decreasing fractionation factors and increasing imino proton chemical shift, δH3. Similarly, a correlation was observed between δH3and deuterium isotope effects (DIE) on chemical shift of thymidine carbon atoms. Combined these results indicate that as hydrogen-bond strength increases the vibrational potential wells of imino protons widen with a corresponding increase in anharmonicity. However, trans-hydrogen bond DIE on carbon chemical shifts of A:T base-paired adenosine residues do not correlate with those measured on thymidine residues. We propose that this lack of correlation is due to DIE dependence on base-pair geometry, which is not easily measured by traditional NMR experiments.

Since the first signs of life on planet earth, organisms have had to adapt to the daily changes between light and dark, and high and low temperatures. This has led to the evolution of an endogenous time keeper, known as the circadian clock. This biological timing system helps the organism to synchronize developmental and metabolic events to the most favorable time of the day. Such a mechanism is of considerable value to plants, since they in contrast to animals cannot change location when the environment becomes unfavorable. Thus is the ability to predict coming events of central importance in a plants life. This thesis is a study of the molecular machinery behind the clockwork in the small weed plant Arabidopsis thaliana as well as its close relative perennial; the woody species Populus. We have characterized a novel component of the circadian clock, EARLY BIRD (EBI). EBI is involved in transcriptional and translational regulation, via interaction with the known post-translational clock regulator ZEITLUPE (ZTL). In Populus, we describe the role of the circadian clock and its components with respect to entry and exit of dormancy and show that gene expression of the Populus LATE ELONATED HYPOCOTYL (LHY) genes are crucial importance for freezing tolerance and thereby survival at high latitudes. Furthermore, the input to the Populus clock is mediated via the phytochrome A (phyA) photoreceptor. / Liv på jorden har alltid behövt anpassa sig till de dagliga växlingarna mellan främst ljus och mörker. Detta har lett till evolutionen av en intern, biologisk klocka, känd som den circadianska klockan, efter latinets ”circa diem”, som betyder ”ungefär en dag”. Denna inre klocka hjälper organismer att styra biologiska processer till den tid på dygnet som är mest gynnsam för deras utveckling och överlevnad. Denna mekanism är av stort värde för växter, eftersom de inte kan söka skydd på mera lämpliga platser om de blir utsatta för olika former av stress. Det gör att förmågan att förutse kommande händelser är av yttersta vikt för växter. Denna avhandling är en studie av det molekylära nätverk som styr denna biologiska klocka i den lilla örtplantan Arabidopsis thaliana (backtrav), och den besläktade träd-arten Populus (hybrid-asp). Vi har karaktäriserat en ny komponent i den circadianska klockan i Arabidopsis, EARLY BIRD (EBI). EBI är involverad i transkriptionell och translationell reglering av klockan, via interaktion med den kända post-translationella klock-regulatorn ZEITLUPE (ZTL). I Populus har vi beskrivit den interna klockan och dess roll i processer som invintring, vinterdvala och återstart av tillväxt. LATE ELONATED HYPOCOTYL (LHY) generna i Populus är avgörande för förvärv av köld-tolerans och således överlevnad på högre latituder. Dessutom har vi visat att signaler till den circadianska klockan i Populus är medierade via fotoreceptorn phytochrome A (phyA).

Norway spruce (Picea abies L. Karst) is a conifer belonging to the group gymnosperms and is an ecologically and economically important species in several parts of Europe. It is crucial for trees like Norway spruce to adapt timing of events such as bud set and growth cessation to the local environment in order to maximize the growth period while avoiding frost damage. This thesis aims at widening the knowledge about genetic control of annual growth rhythm in Norway spruce and particularly the control of bud set. Using spruce transformants ectopically expressing PaFT/TFL1-LIKE 2 (PaFTL2) the prior hypothesis that PaFTL2 induces bud set is confirmed. This is further supported by spatial and temporal expression patterns in seedlings and adult trees. It is further shown that gymnosperms possess at least two FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like genes with TFL1-like function, suggesting the ancestor of FT and TFL1 to be more TFL1-like. PaFTL1 appears to have complementary expression patterns to that of PaFTL2 both spatially and temporally indicating they may act together to control growth in Norway spruce. Since bud set is controlled by photoperiod and circadian clock genes are implicated in this process, putative clock homologs were studied to gain insight into the circadian clock in gymnosperms. Several clock homologs were identified and their expression showed a diurnal pattern but the expression was rapidly damped in constant conditions. Transgenic Arabidopsis expressing putative core clock genes from spruce indicate that at least three genes, PaCCA1, PaGI and PaZTL, appear to have a conserved function between angiosperms and gymnosperms. Taken together these results suggest that gymnosperms have a similar core clock structure as angiosperms even though fundamental differences might exist since the cycling of the clock genes were rapidly damped in free-running conditions. The studies presented in this thesis support substantial conservation of pathway components controlling photoperiodic responses in angiosperms and gymnosperms and identify PaFTL2 as a component of growth rhythm control. However, important changes in these processes are also evident. The results provide a solid basis for future research on molecular mechanisms controlling an adaptive trait in an important non-model organism.

No description available.

Circadian oscillators or clocks are a widespread, endogenous class of oscillatory mechanisms that control the ~24h temporal pattern of diverse organism functions. In cyanobacteria this mechanism is formed by three proteins, KaiA, KaiB and KaiC. KaiA is shown here to be a two domain protein that directly interacts with KaiC and enhances the KaiC autokinase activity. The amino-terminal domain of KaiA can be structurally categorized as a pseudo-receiver, a class of proteins used in signaling cascades and activated by direct protein??protein interactions. The carboxy-terminal domain interacts directly with KaiC, is sufficient to enhance the KaiC autokinase activity in a manner similar to full-length KaiA, and adopts a unique, all α-helical dimeric fold. The structure of this domain raises interesting probabilities regarding the mode of KaiA??KaiC interaction. The two KaiA domains are shown to directly interact with each other, which suggests a possible mechanism of signal transfer from the amino to carboxy-terminal domain. Hydrogen bonds are of paramount importance in nucleic acid structure and function. Here we show that changes in the width and anharmonicity of vibrational potential energy wells of hydrogen bonded groups can be measured in nucleic acids and can possibly be correlated to structural properties, such as length. Deuterium/protium fractionation factors, which are sensitive to the vibrational potential well width, were measured for the imino sites of thymidine residues involved in A:T base pairs or free in solution, and a correlation was established between decreasing fractionation factors and increasing imino proton chemical shift, δH3. Similarly, a correlation was observed between δH3and deuterium isotope effects (DIE) on chemical shift of thymidine carbon atoms. Combined these results indicate that as hydrogen-bond strength increases the vibrational potential wells of imino protons widen with a corresponding increase in anharmonicity. However, trans-hydrogen bond DIE on carbon chemical shifts of A:T base-paired adenosine residues do not correlate with those measured on thymidine residues. We propose that this lack of correlation is due to DIE dependence on base-pair geometry, which is not easily measured by traditional NMR experiments.

No description available.

La rétine contient une horloge endogène régulant différentes fonctions rythmiques et participe à la synchronisation de l'horloge centrale du SCN au temps géophysique. Cette synchronisation met en jeu les bâtonnets, les cônes et les cellules à melanopsine. Contrairement au SCN, le rôle des photorécepteurs dans la réponse à la lumière de l'horloge rétinienne est controversé. Nos travaux et ceux d'autres équipes soutiennent un rôle de la melanopsine alors que 2 études récentes suggèrent que seule la neuropsine est impliquée. Mon projet vise à disséquer le rôle des différents photorécepteurs par des approches in vitro/ex vivo chez des souris sauvages, Per2Luc et/ou déficientes en photorécepteurs. Des lumières monochromatiques ciblant différents photorécepteurs ont été appliquées à des explants rétiniens en culture de souris Per2Luc ou déficientes en melanopsine, cônes MW ou bâtonnets. Nos résultats montrent un rôle des bâtonnets dans le décalage de phase de l'horloge rétinienne par la lumière dans le spectre visible et une contribution additionnelle des cônes SW et/ou de la neuropsine dans l'UV. L'horloge rétinienne étant composée de plusieurs horloges et afin de déterminer leur réponse à la lumière, l'induction photique des gènes Per1-Per2 et C-Fos a été analysée dans les couches rétiniennes isolées chez des souris sauvages et déficientes en photorécepteurs. Chez les souris sans melanopsine ou cônes MW, l'induction de Per1-Per2 est abolie dans toutes les couches, suggérant un rôle de ces photorécepteurs. En résumé, nos résultats indiquent un rôle différentiel des photorécepteurs en fonction de la réponse mesurée (décalage de phase de PER2::Luc et induction des gènes de l'horloge par la lumière) / The mammalian retina contains an endogenous pacemaker regulating retinal physiology and participate to the sybchronization of the temporal phase of the central clock of the SCN to environmental time. This entrainment process involves rods, cones and melanopsin-containing retinal ganglion cells. In contrast with the SCN, the role of these photoreceptors in the light response of the retinal clock is still controversial. While recent studies suggest that none of them is involved in light response of the retinal clock, others support a role for melanopsin. My project aims to dissect the role of these different photoreceptors in wild-type, Per2Luc and/or photoreceptor-deficient mice using in vitro/ex vivo approaches. Monochromatic lights targeting different photoreceptors were applied to retinal explants of Per2Luc or melanopsin-, MW cones- or rods-deficient mice. Our results demonstrate that rods are required for the light-induced phase shift of the retinal clock in the visible spectrum and suggest an additional contribution of SW cones and/or neuropsin in the UV. As the retinal clock is composed of several clocks and in order to determine their response to light, the photic induction of Per1-Per2 and C-Fos genes was analyzed in isolated retinal layers from wild-type and photoreceptor-deficient mice. In mice without melanopsin or MW cones, Per1-Per2 induction by light is abolished in all layers, suggesting a role for these photoreceptors. In summary, our results propose a differential contribution of the retinal photoreceptors as a function of the response recorded (phase shift of PER2::Luc or induction of clock genes by light)

The aryl hydrocarbon receptor (AhR), a ligand-dependent transcription factor, plays a crucial role in regulation of xenobiotic metabolism. AhR is also involved in dioxin-induced metabolic disorders and alteration of circadian rhythm. Furthermore, circadian clock disruption and metabolic dysfunction are integrally associated with each other. This study was designed to understand the mechanisms by which AhR contributes to regulation of circadian clocks, fat metabolism and glucose homeostasis. In the first aim, I have tested whether AhR interacts with the core clock gene, brain and muscle AhR nuclear translocator like-1(BMAL1), disrupting circadian locomotor output cycle kaput (CLOCK)/BMAL1 complex activity, and leading to the suppression of period1 gene (Per1) expression rhythm. My studies indicate that AhR activation by its agonists 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and beta-naphoflavone (BNF) disrupts the rhythm and inhibits the expression of Per1 in mouse liver and hepatoma cell lines, respectively. Mechanistically, the disruption of the rhythm and the inhibition of Per1 expression occur secondary to the interaction between AhR and BMAL1, which attenuates transcriptional activity of the core clock complex CLOCK/BMAL1. These results suggest alteration of the circadian clock as a novel signaling event downstream of AhR activation. The integral relationship between the clock and metabolic function further suggest that AhR activation may cause metabolic dysfunction. In the second aim, I have tested whether AhR activation inhibits Per1 gene induction and influences circadian clock resetting through activation of JNK pathway. AhR activation by it agonists TCDD and BNF decreases light-induced phase shifts in the early night and inhibits light-induced Per1 expression in both suprachiasmatic nucleus (SCN) and liver. Inhibition of Per1 induction results from increased phospho-JNK induced by AhR activation. Taken together, activation of AhR disrupts circadian clock resetting which also could cause metabolic dysfunction. In the third aim, I have tested whether AhR deficiency regulates nuclear receptor peroxisome proliferator-activated receptor a; (PPARa) and alters glucose homeostasis. PPARa, a clock-controlled gene (CCG) that acts as a fat metabolism sensor, is important for lipid metabolism and glucose homeostasis. AhR knockout (AhRKO or AhR-/-) mice exhibit enhanced insulin sensitivity and glucose tolerance, accompanied by decreased expression of PPARa, key gluconeogenic genes, glucose-6 phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PEPCK) and key fatty acid oxidation enzymes, carnitine palmitoyl transferase1b (CPT1b) and acyl-CoA oxidase (ACO). Conversely, AhR agonists increase PPARa; expression in a BMAL1-dependent manner. In addition, AhRKO mice display altered rhythm for clock genes, clock-controlled genes (CCGs) and physiological blood glucose. These data suggest that AhR may modulate the glucose homeostasis through regulation of CCGs such as PPARa and that PPARa may be an important link between the circadian clock and metabolism. In the fourth aim, I have tested the effects of AhR ablation or attenuation in high-fat diet (HFD)-induced obesity, insulin resistance and hepatic steatosis in mice. Recent studies suggest that PPARα expression is elevated with HFD feeding as an adaptive response to attenuate hepatic steatosis, and PPARa deficiency protects against HFD-induced insulin resistance. AhR-/- as well as AhR heterozygous (AhR+/-) mice are protected from the HFD-induced obesity, insulin resistance, hepatic steatosis and show reduced inflammatory cytokine expression. In addition, AhR-/- and AhR+/- mice display protected insulin signaling, a higher adiponectin and a lower leptin and insulin in serum. Food intake and physical activity are not significantly different among WT, AhR-/- and AhR+/- mice with HFD feeding. Indirect calorimetry has demonstrated that the AhR+/- mice have higher oxygen consumption, CO2 production and heat production. In addition, Real-time PCR data show that uncoupling protein 1(Ucp1) is higher in brown adipose tissue which supports the higher heat production; moreover, the muscle gene profile reveals that the fatty acid beta-oxidation genes and mitochondrial respiratory genes are higher in AHR+/- mice which further support higher energy expenditure in these mice. Collectively, these data suggest that AhR signaling could be a potential target for treatment of obesity and type 2 diabetes, and AhR antagonist may be developed into a drug for these metabolic diseases.