Thesis (Ph.D.) in Biological Sciences--University of Maine, 2009. / Includes vita. Includes bibliographical references (leaves 83-96).

Thesis (Ph.D.)--East Carolina University, 2009. / Presented to the faculty of the Department of Physiology. Advisor: Jian Ding. Title from PDF t.p. (viewed June 12, 2010). Includes bibliographical references.

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In mammals, the circadian clock coordinates multiple behavioural and physical processes, including energy homeostasis. At the centre of these rhythms lies the circadian clock machinery, a precisely coordinated transcription-translation feedback system required to maintain the correct time. Metabolic homeostasis requires accurate and coordinated circadian timing within individual cells and tissues of the body. Moreover, recent evidence has shown that the coupling of circadian and metabolic circuits involves reciprocal regulatory feedback. In line with this, mounting evidence suggests that disruption of the clock contributes to the development of obesity and its comorbidities. This is particularly concerning given that modern lifestyles often undermine our bodies’ clock. However, the casual mechanisms which link circadian disruption to metabolic disease are not well defined. This work aims to gain a further understanding of clock control of metabolic homeostasis and especially regulation of lipid metabolism. This work uses dietary challenge to determine which peripheral clocks and downstream metabolic pathways are particularly susceptible to diet induced obesity (DIO). We demonstrate that although behavioural rhythmicity was maintained in DIO, gene expression profiling revealed tissue-specific alteration to the phase and amplitude of the molecular clockwork. Clock function was most significantly attenuated in visceral white adipose tissue (WAT) of DIO mice, and was coincident with elevated tissue inflammation, and dysregulation of clock-coupled metabolic regulators PPARα/γ.The rhythmic expression of Rev-erbα, a nuclear receptor involved in the circadian clock, was particularly affected in DIO mice. This study uses the Rev-erbα-/- mouse to explore clock-metabolic coupling, specifically lipid metabolism. In line with published work, Rev-erbα-/- mice exhibit an obese phenotype with associated upregulation in gWAT of lipogenic (Dgat2, Fasn) and fatty acid liberation (Lpl) genes. Differences in fat mobilization are observed as Rev-erbα-/- mice show a heightened insulin stimulated lipogenic drive and an attenuation of the lipolytic drive in the fasted state, suggesting an increased propensity for fat accumulation. The role of the clock was further investigated in adipose tissue by deletion of Bmal1 (clock ablation) or Rev-erbα (clock manipulation) specifically in adipocytes using Cre-Lox methodology. AdipoCREBmal1flox/flox mice showed attenuated feeding rhythms, indicating a direct effect of the adipocyte circadian clock on hypothalamic feeding centres and severe dysregulation of metabolic genes. However, AdipoCRERev-erbαflox/flox displayed very little phenotypic difference compared to control littermates, suggesting that global loss of Rev-erbα may have reinforcing metabolic consequences. This work suggests a key role of the clock in lipid handling and the pathogenesis of obesity. Insights into this link may lead to novel targets for treating both obesity and metabolic complications.

The aim of this study was to determine the specific interactions among clock gene alleles in Drosophila melanogaster and their effect on the function of the circadian clock. The second part of this study deals with the expression pattern (both temporal and spatial) of two core clock factors known from Drosophila, period and timeless, in the central nervous system of the red flour beetle, Tribolium castaneum.

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In mammals endogenous, self sustained oscillators, known as circadian clocks, have evolved as a result of day night cycles, with a period close to 24 hours, and are involved in many physiological processes; such as sleep wake cycles, metabolic and hormonal activity. The suprachiasmatic nucleus (SCN), is the central oscillator, and is synchronised to the external environment by light, via the eye. It has been demonstrated that peripheral clocks, too, contain the circadian oscillator, with tissues such as the lung, liver, heart and kidney as well as many isolated cell types remaining rhythmic, in culture, for many days. However, these peripheral oscillators require a signal from the central oscillator in order to co-ordinate a synchronised time. Leading candidates in the relay of this information are the circulating glucocorticoid hormones corticosterone (rodents) or cortisol (man), which are known to have potent effects on the peripheral clock, both in-vivo and in-vitro. Further to this, glucocorticoids have been used for many decades to suppress the symptoms of inflammation, a by product of many human diseases.This thesis aims to address the temporal regulation of the peripheral clock by the endogenous glucocorticoid, corticosterone, using a transgenic mouse harbouring a luciferase conjugated clock reporter, and circadian reporter cell lines. It also aims to address the relative contribution of the two closely related nuclear hormone receptors, the glucocorticoid and mineralocorticoid receptors. A further aim of the work with glucocorticoid signalling was to design a flow-though culture system, in order to address the effects of the endogenous pulsatile release of glucocorticoids on the peripheral oscillator. This thesis also aims to characterise the inflammatory response in relation to its circadian characteristics; its relationship with corticosterone and the effect of inflammation on the central clock components. Finally, this thesis aims to investigate a potential input/output of the clock, a member of the family of C/EBP transcription factors, C/EBP alpha, and whether it is under endogenous circadian control and regulated by glucocorticoids.Work in this thesis has shown that glucocorticoids dynamically regulate the peripheral clock at all phases of the circadian cycle and that this regulation occurs mainly through the glucocorticoid receptor; yet the mineralocorticoid receptor does have a function in the immediate response to glucocorticoid administration. Furthermore, as a result of the initial temporal profile after corticosterone addition, on the clock protein PERIOD2, I have shown transient regulation of the clock through Caveolin-1 based signalling. There is also a significant circadian component to the inflammatory response, which appears, at least in part, to be REV-ERB alpha mediated, and the inflammatory response also has profound effects on circadian gene expression in the periphery. A functional flow-through system was designed and a working model produced, albeit with technical difficulties, to address glucocorticoid pulsing and circadian timing but much more work is needed for effects to be fully understood. C/EBP alpha appears not to be under circadian regulation nor under direct glucocorticoid regulation, at least in peripheral models used here.

Anadromous pink salmon undergo several migratory movements between different habitats during their life history. These migrations are accurately timed on a seasonal basis. Annual rhythms or seasonally-timed events may result from interactions between daily rhythms and annual changes in environmental factors. Therefore, knowledge of daily behavioral rhythms in pink salmon may improve our current poor understanding of the seasonal timing of its migrations. Hence, the objective of this study was to investigate, in a seasonal context and mainly under laboratory conditions, diel rhythms of ecologically-relevant behavior in juvenile pink salmon, and their timing mechanisms. Fry emergence from a simulated gravel redd in fresh water was mainly nocturnal below 13°C. Diel emergence timing was synchronized with the onset of night, but was affected by temperature in a non-linear manner. Temperature affected negatively the duration of the intra-gravel alevin stage and the rate of emergence. Nocturnal emergence was considered an anti-predator adaptation. Fry exhibited mainly nocturnal rhythms of swimming activity and of vertical distribution during the first week after emergence. However, a gradual shift from a nocturnal to a diurnal swimming activity rhythm occurred 7 to 13 days after emergence, when wild fish are residing in estuaries and adjacent coastal waters. Coincident with this shift was an increasing tendency of the fry to swimnnear the water surface during the day. This suggested a weakening of their negative phototactic response during this period. Thereafter, the fish usually displayed diurnal rhythms of swimming activity and nocturnal rhythms of vertical distribution. The ontogenetic shift in the phase of the activity rhythm and in photobehavior was considered adaptive for schooling and feeding during the day. Wild fry fed mainly during daylight hours in littoral areas of two marine bays. However, their feeding rhythms varied among study sites. Laboratory experiments showed that hunger level affected fish feeding rate and ration consumed positively. Fish fed continuously on live copepods under idealized laboratory conditions. During a 12-h session they rapidly (< 30 min) filled their stomachs with prey; thereafter, they maintained their stomachs full by feeding at a rate that balanced the rate of evacuation of prey from the stomach. Hence, I concluded that pink salmon have flexible feeding activity rhythms, which may permit opportunistic exploitation of prey, and feed at a relatively low hunger threshold. This feeding strategy may explain in part their relatively high growth rates in nature. During the periods corresponding to their juvenile coastal and pelagic ocean phases, the fish exhibited generally diurnal rhythms of swimming activity and of aggression, and nocturnal rhythms of vertical distribution in response to simulated seasonal photoperiodic and temperature changes. These rhythms were synchronized with the artificial light-dark (LD) cycle throughout most of the year. Some parameters of these rhythms varied on a seasonal basis, but not according to the Aschoff-Wever model. Mean swimming speed, the degree of diurnalism of the swimming activity rhythm, and the timing of the daily peak of the rhythms were affected by daylength. Hence, photoperiod might be an important proximate factor that pink salmon use to time their oceanic migration on a seasonal basis. Some data suggested the existence of an endogenous, circadian activity rhythm, and thus a daily "clock", in pink salmon. However, this remains uncertain. The free-running period of their activity rhythm was not related negatively to constant light intensity, as predicted by the Circadian Rule. The LD cycle affected directly swimming activity (masking), rather than entraining an endogenous circadian system. Since the activity rhythm of pink salmon does not possess a strong endogenous component, it is doubtful that the seasonal timing of its migrations results from interactions between a circadian clock and seasonal changes in environmental factors. However, the flexibility and inter-individual variability of their behavioral rhythms may be adaptive responses to the instability and heterogeneity of the marine environment. / Science, Faculty of / Zoology, Department of / Graduate

The day-to-day physiologies are largely influenced by circadian rhythms. Disruptions of such rhythms are associated with many diseases. Adjusting them to a healthy one can be promising to treat different circadian rhythms disruption associated diseases such as sleep disorders, cardiovascular disorders, metabolic disorders. The regulations underlying the circadian rhythms are much complicated and systematic which may involve thousands of genes. In mammals, these robust circadian rhythms are primarily intended by the concerted molecular interplays, knowingly, transcriptional-translational feedback loops (TTFLs). The collaborative interactions among a large number of genes intend to sustain the TTFLs. It facilitates to generate the primary transcriptional oscillations among the clock genes and genome-wide rhythmic oscillations. The collaborative transcriptional events act as dominant driving forces underpinning such rhythmic expressions. The mode of the transcriptional regulations depends on the concentration of the transcriptional factors (TFs) at the promoter region at a particular time point. The inclusive mechanisms of their regulations and the associated circadian rhythmic outputs across the physiology are not well defined yet. However, temporal recruitment of core-clock proteins, different transcriptional and translational regulators and chromatin modifications are imperative towards a comprehensive understanding of the spatio-temporal regulation of such complex rhythms. Despite many experimental signs of progress about the circadian transcriptional controls, there is still an interesting question remains unexplored that how do these few components belonging to the same molecular architecture are capable to govern such divergent gene expressions? Nevertheless, how they are being regulated and the landscape of their combinatorial regulatory controls have not gained any inclusive attention yet. Thus, a systematic understanding considering all-encompassing circadian TFs and their relational interplay could help us to decode the intricated transcriptional regulatory logics composed by different TFs. Such comprehensive understanding may lead to unleashing their potential to therapeutically modulate the circadian rhythms. Experiments alone are indeed quite challenging to achieve this. Decoding the inclusive transcriptional insights along with multifaceted molecular regulations remained out of reach with prevailing approaches. They are limited by the complexities of more integrative algorithms that accommodate different layers of molecular information quantitatively into a single framework. Studies indicated the knockout of the circadian TFs results in changing the rhythms. And, rescuing them helps to regain the circadian functionality substantially. However, knocking out all possible combinations of circadian TF-genes experimentally is merely very tedious, time-consuming and expensive. And, some essential genes cannot be knocked out. The magnitude of disruption of the circadian rhythmic fluctuations may also vary in disease conditions and even from individual to individual. These are serious concerns which were weakly understood. Due to the lack of advanced quantitative approach, these have remained a great challenge with traditional practices for reversing the disrupted circadian rhythms. Another level of challenge is not only aligning the rhythms but also, having a strong understanding of the directionality of the alignment varying in different clinical contexts is the most crucial. Consequently, a thorough quantitative understanding at the molecular level of the clock control mechanisms is essential. To address these ambiguities, a quantitative understanding of the circadian gene regulation and the molecular interplay among the key regulators are quite important. An alternative yet the operative approach is the reconstruction of transcriptional network with those genes having circadian fluctuations by computational simulations. It may capture a systematic snapshot of such gene regulation network at a dynamic scale. Inferring them is again a complicated task as the large numbers of variables are unknown in the systems. There is also a lack of tools to capture and integrate the dynamic view which is biologically relevant. Virtual knockout experiments leverage in inferring such dynamic transcriptional regulatory networks iteratively and effectively. The molecular machinery underpinning the circadian rhythms possess high-temporal resolutions. Thus, it is also quite challenging to construct the network of those genes under the influence of TTFLs at dynamic scale using existing methods. Most of the prevailing approaches are quite limited by the quantitative understanding of the transcriptional landscape thoroughly. Recently, one of our computational approaches, LogicTRN was proposed for modelling the transcriptional regulatory networks quantitatively. Deploying the high-resolution temporal gene expression data and the TF-DNA binding data, it calculates the TF-DNA binding occupancy, which is a quantitative estimation. It also predicts the all possible combinatorial TF-logics influencing those target genes' regulations. Here, we introduced an extended computational approach based on LogicTRN to decode the quantitative transcriptional regulatory landscapes of circadian genes. We introduced the reconstruction of quantitative transcriptional regulatory networks (qTRNs) for circadian gene regulations using LogicTRN framework. The qTRNs facilitated to discover a wide range of genes exhibiting circadian fluctuations. Their dynamic behaviours and the cis-regulatory logics in the networks were also estimated precisely. Based on quantitative knowledge from qTRNs, we have further developed a method for virtually knocking out the core clock component TFs to estimate the influence to perturb the circadian rhythmic fluctuations at a dynamic scale. Consecutively, the method of single/multiple genes virtual knockout was developed and used to screen the best TF/TFs combination that effectively modulates the circadian rhythmic output at a dynamic scale. They were also ordered by their influence to perturb the circadian fluctuations in the qTRNs. In future, it may indicate a way to target the molecular regulators to therapeutically modulate the circadian period lengths in a specific direction based on an individual's clinical conditions. Our results indicate the reconstruction of highly accurate quantitative regulatory networks for the transcriptional controls of the circadian gene regulation at a dynamic scale. We have also identified the best plausible transcription factors or their combinations those can effectively modulate the circadian rhythms. Of them, the CLOCK and CRY1 double knockout preserve the highest capacity to modulate the circadian rhythm dynamics. Besides, all possible TFs/TF-combinations were ordered in terms of their capacity to influence the qTRNs at dynamic scales. Finally, our quantitative framework offers a quick, robust, and physiologically relevant way to screen and identify the most effective TFs/TF-combinations to modulate circadian rhythms. This foundation may potentially enable us to engineer the molecular regulators underpinning the circadian rhythms. This potentially indicates a clue towards adjusting the circadian rhythmic phases in desired directions depending on clinical requirements