Almost all organisms have an endogenously generated and self-sustained time-keeping system that oscillates with a periodicity of about 24 h, namely the circadian clock, that help them adapt to daily environmental changes. Mammalian circadian rhythms are generated and maintained by transcription-translation feedback loops (TTFLs) and include post-translational modifications to help fine-tune the oscillation. Circadian rhythms control a broad range of cellular signaling pathways including those mechanisms involved in cell division and DNA damage response (DDR). We have previously established that the core clock component PERIOD2 (PER2) binds to the tumor suppressor protein p53, a key regulatory checkpoint component that modulates cell cycle progression and the cellular response to genotoxic stress. PER2 binding to p53 modulates p53's stability, cellular localization, and transcriptional activity. As described in Chapter 2, we now identified PER2 as a previously uncharacterized substrate for the ubiquitin E3 ligase mouse double minute 2 homolog (MDM2), an oncoprotein and negative regulator of p53. Our findings showed that the association between PER2 and MDM2 is independent of the presence of p53. In addition, MDM2 targets PER2 for ubiquitylation and degradation in a phosphorylation-independent fashion. Lastly, our studies showed that MDM2 collaborates with β-transducin repeat-containing proteins (β-TrCPs), an E3 ligase that targets PER2 for ubiquitylation in a phosphorylation-dependent manner, to control PER2 degradation and thus the length of circadian period. Because the p53:MDM2 pathway plays a critical role in the cellular response to genotoxic stress, the project described in Chapter 3 is based on the hypothesis that DNA damage caused by radiation shifts the circadian clock phase via the p53:PER2:MDM2 complex. Firstly, we generated Trp53KO (Trp53 gene encodes mouse p53) cell lines in NIH 3T3 Per2:dLuc reporter cells expressing luciferase driven by the Per2 promoter. Phase-response curves (PRCs) for Trp53WT and Trp53KO reporter cells were obtained in response to ionizing radiation (IR) treatments. Results indicated that Trp53 knockout did not affect radiation-induced circadian phase shifts, whereas increased p53 levels induced by transient inhibitor treatments prevented phase shifts when IR was performed at the trough of PER2 abundance. Additional mechanisms were unveiled that kinases ATM (Ataxia Telangiectasia Mutated), ATR (ATM- and Rad3-related) and CHK2 (Checkpoint Kinase 2) regulate radiation-induced phase shifts. Lastly, we found that CLOCK (Circadian Locomotor Output Cycles Kaput) and CRY1 (CRYPTOCHROME 1) were phosphorylated in response to radiation. Taken together, these results indicate that radiation-induced clock phase shifts involve the activity of kinases ATM, ATR and CHK2, and the modification in CLOCK and CRY1. Chapter 4 is a review of current findings about the interaction between circadian rhythms and the cell division cycle regulation pathway. The article highlights a multidisciplinary approach that combines mathematical modeling and experimental data to reveal how p53:PER2:MDM2 acts as a node controlling timely cell cycle progression. In summary, our work provided evidence that MDM2 targets PER2 for ubiquitylation and degradation in a phosphorylation-independent manner, and this influences circadian oscillation. Furthermore, the exploration of p53:PER2:MDM2 association shed light on how radiation-induced DNA damage shifts clock phase. These findings expose a crosstalk mechanism that senses DNA damage and shifts the clock system. / Doctor of Philosophy / Mammals have a time-keeping system that oscillates with a periodicity of about 24 h, namely the circadian clock, that allows physiological and behavioral adaptation to environmental changes. The circadian clock controls and coordinates processes as diverse as sleep/wake cycle, feeding cycle, daily changes in body temperature, blood pressure and hormone secretion. At the cellular level, the circadian clock exists in almost all cells and controls a broad range of cellular signaling pathways including mechanisms involved in cell division and DNA damage response (DDR) pathway. Circadian disruption, for example, by night shift work, results in accumulation of DNA damage in cells and increases risk of cancer. In my thesis, we found that MDM2, a protein that is involved in the DDR signaling pathway and has the potential to cause cancer, controls the degradation of the core clock protein PERIOD2 (PER2), and thus regulates the length of circadian period. Further work exposed the mechanism for how DNA damage shifts the circadian clock. Our findings will have significant impacts on health and biomedical science, especially shedding light on optimizing the time in a day to give chemo- and radiation therapies to cancer patients.

Circadian rhythms are daily molecular oscillations within cells ranging from prokaryotes to humans. This rhythm is self sustaining, and receives external cues in order to synchronize an organism's behavior and physiology with the environment. Many metabolites utilized in metabolic processes seem to follow a pattern of circadian oscillation. Iron, an essential component in cellular processes such as respiration and DNA synthesis, is obtained almost exclusively through diet, yet little is known about how the clock governs iron metabolism. The regulation of iron within the cell is very tightly controlled, as iron is highly reactive in the generation of oxidative stress and the excretion of excess iron is very limited. There are limited findings indicating that there are molecular ties between the circadian clock and the regulation of iron metabolism. The first half of my dissertation focuses on the role of the circadian clock in modulating expression of iron metabolic components. We found that key components of iron import, in TFRC, and export, in SLC40A1, show altered expression in response to changes in the expression of clock transcription components. Furthermore, in circadian synchronized HepG2 hepatocytes TFRC and SLC40A1 showed rhythms in their mRNA expression, although expression of these genes was highly altered in conditions of high iron availability. We also examined IREB2, which expresses a master regulator of iron concentration in IRP2. IRP2 showed rhythms in phase with circadian component PER2, and IRP2's rhythmicity was lost under iron overload conditions. We observed that the ability of these three critical iron metabolic components to respond to sudden increases in available iron was mitigated in cells with clock impairment. Whole cistrome and transcriptome analysis was used to determine that rhythmicity in TFRC and SLC40A1 are not equal in their recruitment of circadian protein binding or in the stage of transcription in which circadian rhythms are generated. The cumulative effect of all of this regulation is that rhythmic variation in intracellular hepatic ferrous iron is clock controlled. The second half of my dissertation focuses on understanding how iron uptake influences clock resetting. Initially, iron was added to the cells in the form of ferrous sulfate, or chelated out of the cells using 2-2'-dipyridyl and clock gene expression was monitored. Altered rhythmicity of these components was seen at both the mRNA and protein level in cells with disrupted iron homeostasis. Then, we measured changes in period, phase, and amplitude of these rhythms, ultimately using a luciferase reporter cell line to demonstrate that even slight changes in cellular iron produce an effect on rhythmic period. We find that the circadian clock and iron metabolism pathway are intimately related, and that the intracellular iron concentration plays a role in circadian clock behavior. Overall, our research illustrates the importance of the circadian clock in liver metabolism and physiology. Improper iron metabolism due to genetic or dietary shortcomings is common in humans, and our work builds on the importance of chronotherapy in treatment of these conditions. Conversely, our research into the effect intracellular iron has on the clock contributes to the growing body of research into how circadian clocks, especially the peripheral clock of the liver, receive input from a range of metabolites in conjunction with signals from the master oscillator of the suprachiasmatic nucleus. / Ph. D.

Artificial lighting at night is a growing worldwide phenomenon that can negatively impact flora and fauna in the surrounding area. With new technology, there is now opportunity for change: newer LEDs can emit specific wavelengths of light that may be less ecologically damaging. In this study, we aim to describe the circadian spectral sensitivity of two phylogenetically distant urban spider species with similar life histories, the Araneoid Parasteatoda tepidariorum and non-Araneoid Pholcus manueli, to determine differences between them. We exposed these spiders to progressively dimmer levels of white, blue, green, or red light. Despite evidence that spiders lack visual sensitivity to red light, we found that not only could both species entrain to the dimmest red light, P. tepidariorum had stronger entrainment to green and red light than white light. This study suggests that wavelength selection for ALAN will require a nuanced approach considering the sensitivities of individual local species.

The aetiology of bipolar disorder remains unclear and investigation to date has focussed largely on bipolar patients. Whilst ultimately of huge value, such studies may also be confounded by current mood or experience of repeated illness episodes or current or past medication; using at-risk samples may bypass some of these problems. The current research therefore assessed the efficacy of the Mood Disorder Questionnaire (MDQ) as a screening tool for vulnerability to bipolar disorder. The MDQ was used with two sets of criteria to identify two sub-groups of medication-naïve young bipolar phenotype subjects who were at risk for bipolar disorder by virtue of experience of mood elevation. Analysis of data from the Student Stress Survey was carried out to characterise the bipolar phenotype. Compared to a control group with no experience of mood elevation, the two bipolar phenotype sub-groups showed a gradient of prevalence of bipolar diagnosis and associated co-morbidity. Behavioural and functional magnetic resonance imaging (fMRI) techniques were employed to investigate emotional processing, decision-making, and sleep and circadian rhythmicity in bipolar phenotype students. Analyses revealed that positive emotional processing biases, disrupted decision-making, and increased activity during sleep were associated with the bipolar phenotype and, therefore, may represent vulnerability markers for bipolar disorder. Finally, a psychopharmacological investigation of quetiapine, which stabilises mood, was carried out in healthy volunteers. One-week quetiapine administration resulted in biases away from both positive and negative emotional stimuli (i.e. a mood-stabilising effect), reduced discrimination between different magnitudes of gains and losses during risky decision-making (consistent with an antidepressant effect), and increased sleep duration. In sum, this research has developed our understanding of vulnerability markers associated with the bipolar phenotype and provided a first step towards uncovering the psychological mechanisms through which quetiapine’s clinical effects may be mediated.

The circadian rhythm is a rhythm which permeates all aspects of biological life and follows the hours of the sun. The pace of the rhythm is controlled by a collection of neurons in the hypothalamus, called the suprachiasmatic nucleus (SCN), whose signals affect rhythms throughout the body as can be seen in aspects of life from behavior down to oscillations of proteins in the cells. A disruption of this rhythm such as what happens during jet lag, where the rhythm of the SCN is out of synch with the rhythm of the rest of the body, is something that can have adverse effects on mental and physical health. To realign the SCN and the rhythm of the body, different methods and be implemented. This thesis investigated the effectiveness of glucocorticoids on re-aligning the rhythms of the body following a disruption through a meta-analysis and a qualitative review. The meta-analysis and review incorporated experiments from six articles investigating the hours of circadian rhythm shifts in the mouse model, after administering glucocorticoids. What was found was that the individual experiments presented results with high effect sizes; however, the direction of said effects was not uniform as the rhythms shifted in different directions. The lack of uniform direction caused no significant combined effect size to be found by this meta-analysis (MES=0.11 ± 0.06), showing that a statistical analysis based on hours shifted could not find a significant combined effect. The qualitative review, however, indicates that the administration of glucocorticoids shows an effect in re-entraining the rhythm of the peripheral parts of the body to that of the environmental cues and the SCN. Though no significant statistical effect was found in this analysis, the effect of glucocorticoids should not be discounted and could still prove a promising treatment for circadian disruptions, such as jet lag.

Objetivo: Avaliar a relação do turno escolar e o ritmo circadiano de crianças e adolescentes sob a expressão de sintomas comportamentais e de níveis de cortisol e melatonina. Métodos: Estudo transversal envolvendo 639 estudantes do ensino fundamental e médio (idade média de 13,03 anos, variando de 8–18; 58,5% meninas) recrutados em cidades localizadas na região do Vale do Taquari, Rio Grande do Sul, Brasil. Na segunda fase, 80 participantes foram selecionados aleatoriamente para coleta de saliva para análise de melatonina e cortisol. Os parâmetros circadianos do sono foram acessados pelo auto-relato de duração do sono nos dias de semana e fins de semana, diferenças no horário de acordar e dormir, déficit de sono, ponto médio do sono nos dias de semana e fins de semana, jetlag social e pela versão em português do Morningness-Eveningness Questionnaire (MEQ) para avaliação do cronotipo. Os desfechos, níveis de melatonina e cortisol salivares, foram medidos através de amostras de saliva pela manhã, tarde e noite, e problemas de comportamento (sintomas psiquiátricos), foram avaliados usando a Lista de verificação comportamental para crianças e adolescentes (em inglês, Child Behavior Checklist, CBCL). O estudo foi realizado de acordo com as diretrizes éticas internacionais (número de aprovação no comitê de ética: 12-0386 GPPG/HCPA). Resultados: No primeiro artigo, estudantes do turno da manhã eram significativamente mais velhos, apresentavam maior diferença entre os horários de acordar e dormir, maior déficit de sono e jetlag social. O déficit de sono apresentado por meninas foi maior do que o observado em meninos da mesma idade. regressão multivariada, utilizando o método passo-a-passo, identificou jetlag social, diferença nos horários de acordar nos dias de semana e fins de semana e ponto médio nos fins de semana como preditores significativos de déficit de sono. O segundo artigo demonstrou que o turno escolar influenciou a secreção de melatonina, a qual se correlacionou com os parâmetros do sono circadianos, diferentemente para o grupo não-clínico e clínico. Os níveis de melatonina foram positivamente correlacionados com ponto médio do sono em estudantes do turno da manhã, e negativamente correlacionados com ponto médio do sono em estudantes do turno da tarde. No terceiro artigo, identificou-se idade, horário de início da escola, ponto médio de sono e duração do sono nos dias de semana como preditores de sintomas psiquiátricos, avaliados pelo CBCL. Os estudantes do turno da manhã, classificados como cronotipo do tipo vespertino, apresentaram menor duração do sono durante a semana e maior jetlag social do que estudantes do tipo matutino. Além disso, os alunos do turno da manhã com sintomas psiquiátricos apresentaram menor duração do sono e padrão circadiano de sono mais cedo. Conclusões: Os achados do presente estudo mostram que o turno escolar influencia os parâmetros circadianos de sono, fatores fisiológicos e sintomas psiquiátricos em crianças e adolescentes. Nossos resultados reforçam a importância de redirecionar crianças e adolescentes para um turno escolar que contemple as preferências individuais de sono, prevenindo as consequências negativas à saúde, tanto no sono quanto em sintomas psiquiátricos. / Objective: To evaluate the relationship of the school schedules and the circadian rhythm of children and adolescents under the expression of behavioral symptoms and cortisol and melatonin levels. Methods: This cross-sectional study involved 639 elementary and high school students (mean age 13.03 years, range 8–18, 58.5% female) recruited from the cities located in the Vale do Taquari region, Rio Grande do Sul, Brazil. In the second phase, 80 participants were randomly selected for saliva collection to analyze melatonin and cortisol. Circadian sleep parameters were assessed by self-reported sleep duration on weekdays and weekends, bedtime and wake time differences, sleep deficit, midpoint of sleep on weekdays and weekends, social jetlag, and the Portuguese version of Morningness-Eveningness Questionnaire (MEQ) for assessment of chronotype. The outcomes, salivary melatonin and cortisol levels, were measured in morning, afternoon, and night saliva samples, and behavior problems (psychiatric symptoms) were assessed using the Child Behavior Checklist (CBCL). This study was performed according to international ethical guidelines (ethics committee approval number: 12–0386 GPPG/HCPA). Results: In the first article, the morning-school-time students presented significantly higher age, bedtime and wake up differences, sleep deficits, and social jetlag. The sleep deficit presented by girls was greater than that observed in boys of the same age. A step-by-step multivariate logistic regression identified social jetlag, the difference between waking times on weekdays and weekends, and the mid-point of sleep on weekends as significant predictors of sleep deficit. In the second article, school start time influenced the melatonin secretion, which correlated with circadian sleep parameters, although differently for non-clinical and clinical groups. Melatonin levels were positively correlated with sleep midpoint in morning students, and negatively correlated with sleep midpoint in afternoon students. In the third article, we identified age, school start time, midpoint of sleep on weekdays, and sleep duration on weekdays as predictors of psychiatric symptoms, as evaluated by the CBCL. Students with a morning school start time whose chronotype was classified as evening had shorter sleep duration on weekdays and higher social jetlag than morning-type participants. Moreover, students with a morning school start time and psychiatric symptoms had shorter duration of sleep and earlier circadian sleep patterns. Conclusion: The findings of the present study showed that school start time influences on the circadian sleep patterns, physiological factors and psychiatric symptoms in children and adolescents. Our findings emphasize the importance to redirect children and adolescents for a school start time that includes the individual preferences of sleep, preventing the negative health consequences, both in sleep and in psychiatric symptoms.

Ces dernières années ont vu le développement du commerce international entraînant une accélération des mouvements intercontinentaux d'espèces. Ces multiples introductions sont à l'origine de nombreux cas d'invasion, où les espèces s'établissent et se dispersent. Dans le nouvel environnement, étudier les facteurs liés à la niche écologique permet de comprendre comment se déroule l'établissement des espèces introduites au sein de la communauté d'espèces résidentes. L'hypothèse de la niche vide, qui prédit que l'invasion est possible car un espace vide existe au sein des niches écologiques de la communauté résidente, est un des facteurs facilitants de nombreux cas d'invasion. Par ailleurs, la stratégie d'exploitation de la ressource par l'espèce invasive au sein de la niche écologique peut aussi expliquer la propension d'une espèce à envahir ou non le nouvel environnement. L'objectif de cette thèse est d'explorer l'importance de ces hypothèses dans le succès invasif, au travers de l'exemple de Drosophila suzukii. Introduite en 2008 en Europe et aux Etats-Unis, cette espèce a envahi chacun des continents en moins de 7 ans. Elle est la seule espèce européenne de drosophiles capable de pondre à l'intérieur de fruits sains omniprésents, au sein d'une niche écologique vide de tout compétiteur. Elle est à l'origine de gros problèmes pour la culture de fruits cultivés et se retrouve être l'un des ravageurs majeurs en production de fruits rouges. Mieux comprendre son invasion, sa niche écologique et sa stratégie de sélection d'habitat permet de mieux lutter contre l'insecte, notamment par des méthodes permettant de perturber la localisation des fruits dans l'environnement. Cet aspect appliqué est aussi un objectif important de cette thèse CIFRE, financée pour optimiser la lutte par piégeage massif / In the last few decades, the development of international trade has seen resulting in an acceleration of intercontinental movements of species. These multiple introductions are the cause of many cases of invasion, where species are established and spread. In the new environment, studying factors related to the ecological niche help understanding what happens during the establishment of introduced species within the community resident species. The “empty niche hypothesis”, which predicted that the invasion is possible because a gap exists in the ecological niches of the resident community, is one of the facilitating factors of many cases of invasion. In addition, the strategy of utilization of the resource by the invasive species in the ecological niche may also explain the propensity of a species to invade or not the new environment. The objective of this thesis is to explore the significance of these assumptions in the invasive success, through the example of Drosophila suzukii. Introduced in 2008 in Europe and the US, this species has invaded every continent in less than 7 years. It is the only European species of fruit flies that can lay eggs inside healthy fruits, which are omnipresent, in an ecological niche free of any competitor. It is the cause of dreadful issues for grown fruit and is one of the major pests in production of berries. Better understand its invasion, its ecological niche and habitat selection strategy help better fighting the insect, including methods to disrupt the location of fruit in the environment. This applied context is also an important aspect of this thesis, funded also to optimize the fight by mass trapping

Introdução: O reconhecimento da importância da nutrição enteral em pacientes hospitalizados gerou novos métodos de administração, o que leva a muitas perguntas: quais são os efeitos cronobiológicos da terapia nutricional contínua ou intermitente? Objetivo: O objetivo deste estudo foi avaliar o efeito do horário de administração da nutrição enteral como Zeitgeber do ritmo biológico no gasto energético e consumo de oxigênio, mensurados por calorimetria indireta. Métodos: Ensaio clínico randomizado, realizado de dezembro de 2009 a novembro de 2010, em 34 pacientes com doença neurológica, com idade entre 52 e 80 anos, alimentados através de uma sonda nasoenteral, 15 através de infusão contínua por 24 horas/dia e 19 em quantidades comparáveis de forma intermitente, a cada 4 horas, dás 8 às 20 horas. Foram realizadas 4 medidas de calorimetria indireta nas 24 horas (A: 07:30 h, B: 10:30 h, C: 14:30 h e D :21:30 horas), durante 3 dias, para cada paciente. Resultados: A idade média foi de 69,5±8,50% eram do sexo masculino, IMC 22 ±3,9 kg/m²(homens) e 25±5,6 kg/m²(mulheres). O gasto energético e o consumo de oxigênio mostrou diferença significativa entre os grupos contínuo e intermitente: 1478±817 kcal/24h, (IC: 1249 – 1706), 1782±862 kcal/24h (IC: 1579 – 1984) (p=0.05); 212±117 ml/min (IC: 179 – 245); 257±125 ml/min (IC: 227 – 286) (p=0.048), respectivamente. No gasto energético e consumo de oxigênio diferenças estatisticamente significativas foram encontradas entre as mensurações A, B, C e D em ambos os grupos. Comparando o gasto energético e consumo de oxigênio entre os grupos por Mann-Whitney, houve uma diferença estatisticamente significativa em tempo B e C (p = < 0,01). Conclusão: Foi observado neste estudo uma variação circadiana do gasto energético e consumo de oxigênio nos dois métodos de administração da nutrição enteral, sugerindo que apenas uma medida de calorimetria indireta no dia não é capaz de mostrar a verdadeira necessidade do paciente. Observamos também que o gasto energético foi mais elevado à noite nos dois métodos de administração da alimentação. Além disso, o gasto energético e o consumo de oxigênio foi maior no método de administração intermitente em todos os tempos. / Introduction: The importance of enteral nutrition has grown in recognition resulting in new methods of administration. That leads to many questions such as: what are the chronobiologic effects of continuous or intermittent nutrition therapy? Objectives: The aim of this study was to evaluate the use of enteral nutrition as a Zeitgeber of biological rhythm. Energy expenditure and oxygen consumption were measured by indirect calorimetry in continuous or intermittent nutrition patterns. Methods: A randomized clinical trial was conducted from December 2009 to November 2010. Thirty four neurological patients received through the same kind of calibrated nasogastric tube the standard protein and energy intakes calculated for each subject, 15 through continuous infusion for 24 hours/day and 19 intermittently in comparable quantities, every 4 hours, from 8:00 to 20:00 h. Four indirect calorimetry measures were carried out during the 24 hours (A: 07:30h, B: 10:30h, C: 14:30h and D: 21:30h), for 3 days, for each patient. Results: The mean age was 69.5±8, 50% were male; BMI 22±3.9kg/m² (men), 25±5.6 kg/m² (women). Energy expenditure end oxygen consumption presented a significant difference between the continuous and intermittent groups (1478±817 kcal/24h, (CI: 1249 – 1706), 1782±862kcal/24h (CI: 1579 – 1984) (p=0.05); 212±117 ml/min (CI: 179 – 245); 257±125 ml/min (CI: 227 – 286) (p= 0.048), respectively). In the energy expenditure and oxygen consumption, statistically significant differences were found between the A, B, C and D measures in both groups. By comparing the energy expenditure and the oxygen consumption between the groups by the Mann-Whitney test a statistically significant difference was observed for times B and C (p=< 0.01). Conclusion: A circadian variation of energy expenditure and oxygen consumption was observed in both enteral nutrition administration methods used in this work, suggesting that only one indirect calorimetry measure per day is not able to show the patient’s true needs. It was also observed that the energy expenditure was higher at night in both food administration methods. Moreover, the energy expenditure and oxygen consumption was higher in the intermittent administration method in all times.

<p>In the present studies, aspects of some disease activity measures in rheumatoid arthritis (RA) have been investigated, including the effect of glucocorticoids on this activity. In RA, serum interleukin(IL)-6 levels were elevated and were shown to have a circadian rhythm, with peak levels in the morning, declining towards low or normal levels in the afternoon and evening. In contrast, serum levels of tumour necrosis factor(TNF) alpha were low and stable. In other connective tissue diseases, serum TNF alpha levels were elevated but without circadian variation, while IL-6 levels were low and stable. Nocturnal administration (at 2:00 a.m.) of low-dose prednisolone a few hours before the early morning peak of IL-6 was shown to be significantly more effective in reducing clinical symptoms of disease activity and serum IL-6 levels than the traditional morning administration (at 7:30 a.m.) of the same dose of prednisolone. Circulating monocytes are activated in RA, expressing receptors related to adhesion and phagocytosis. Treatment with glucocorticoids suppressed the expression of these receptors on monocytes, and this may be one mechanism of the beneficial effect of glucocorticoids in RA. Endogenous levels of cortisol seem to play a minor role in expression of monocyte receptors. The different acute phase markers used to assess disease activity in RA showed good corrrelations with each other and with serum IL-6 levels. There were especially strong corrrelations between C-reactive protein (CRP) and Serum amyloid protein A (SAA), and between fibrinogen and erythrocyte sedimentation rate (ESR). Fibrinogen and CRP showed stronger correlation than ESR with the Modified Health Assessment Questionnaire (MHAQ) score and with the neutrophil count. Four simple objective function tests were each compared with the HAQ score a with a radiological joint damage score (Larsen score). The objective function tests correlated with the MHAQ score, and each of these two methods of assessing physical disability correlated with pain, CRP and ESR. In addition, most of the objective function tests correlated significantly with radiological joint damage, while the MHAQ score did not.</p>

Recent research in experimental and computational biology has revealed the necessity of using stochastic modeling and simulation to investigate the functionality and dynamics of gene networks. However, there is no sophisticated stochastic modeling techniques and efficient stochastic simulation algorithms (SSA) for analyzing and simulating gene networks. Therefore, the objective of this research is to design highly efficient and accurate SSAs, to develop stochastic models for certain real gene networks and to apply stochastic simulation to investigate such gene networks. To achieve this objective, we developed several novel efficient and accurate SSAs. We also proposed two stochastic models for the circadian system of Drosophila and simulated the dynamics of the system. The K-leap method constrains the total number of reactions in one leap to a properly chosen number thereby improving simulation accuracy. Since the exact SSA is a special case of the K-leap method when K=1, the K-leap method can naturally change from the exact SSA to an approximate leap method during simulation if necessary. The hybrid tau/K-leap and the modified K-leap methods are particularly suitable for simulating gene networks where certain reactant molecular species have a small number of molecules. Although the existing tau-leap methods can significantly speed up stochastic simulation of certain gene networks, the mean of the number of firings of each reaction channel is not equal to the true mean. Therefore, all existing tau-leap methods produce biased results, which limit simulation accuracy and speed. Our unbiased tau-leap methods remove the bias in simulation results that exist in all current leap SSAs and therefore significantly improve simulation accuracy without sacrificing speed. In order to efficiently estimate the probability of rare events in gene networks, we applied the importance sampling technique to the next reaction method (NRM) of the SSA and developed a weighted NRM (wNRM). We further developed a systematic method for selecting the values of importance sampling parameters. Applying our parameter selection method to the wSSA and the wNRM, we get an improved wSSA (iwSSA) and an improved wNRM (iwNRM), which can provide substantial improvement over the wSSA in terms of simulation efficiency and accuracy. We also develop a detailed and a reduced stochastic model for circadian rhythm in Drosophila and employ our SSA to simulate circadian oscillations. Our simulations showed that both models could produce sustained oscillations and that the oscillation is robust to noise in the sense that there is very little variability in oscillation period although there are significant random fluctuations in oscillation peeks. Moreover, although average time delays are essential to simulation of oscillation, random changes in time delays within certain range around fixed average time delay cause little variability in the oscillation period. Our simulation results also showed that both models are robust to parameter variations and that oscillation can be entrained by light/dark circles.