The primary objective of this paper is to present a computerized method for the extraction of phase shifts from an angular distribution. This was accomplished using a least squares curve fitting routine.

Coral reefs are priority habitats which are vulnerable to natural and anthropogenic disturbances. These can cause phase shifts from coral habitat to degraded algal-dominated states – and consequent changes in the distribution, abundance and activity of associated fish species. In the eastern Red Sea, human-induced reef degradation is likely to increase with planned development of the Saudi Arabian coast and the changing climate. The present study therefore investigates the ecological effects of coral-algal phase shifts in reef-associated fish communities, using naturally occurring within-reef benthic zones as proxies for levels of habitat health - with a focus on how these responses differ temporally. These zones were dominated by: hard coral (coral zone), coral and turf algae (transition zone), and macroalgal canopies (algal zone). Six inshore reef areas, were studied in periods with low and high densities of Sargassum in the algal zones (May and November respectively). Community composition was assessed via visual census and predation activity predicted using two proxies: in situ experiments and biomass of carnivores. In both periods, we observed distinct fish communities in each zone - with reduced species richness, Shannon-Wiener diversity and predation intensity, from the coral to the algal zones. Decreases in the abundance and biomass of fish also occurred from the coral to algal zones in May but a spike, as well as a shift in community composition, occurred in the algal zone in November. This shift is attributed to the vast increases in grazer biomass, predominantly Siganus luridus, associated with the November bloom of Sargassum canopies. The present study established, the composition and functioning of Red Sea fish communities is spatially and temporally affected by increased macroalgal dominance. This finding supports the need for herbivorous fish to be made a conservation priority in the management and conservation of reef systems in order to prevent phase shifts to algal dominated states. We conclude that if Red Sea reefs are allowed to shift to alternate states, depending on the density of macroalgal canopies, reefs may support high biomass and abundance of fish but the functioning of the fish community will be altered and the diversity lost.

Tropical coral reefs provide important ecosystem goods and services that are supported by one or more ecosystem functions (e.g., recruitment, primary production, calcification, and nutrient recycling). Scleractinian corals drive most of these functions, but a combination of global and local anthropogenic stressors has caused persistent shifts from coral- to algae-dominated benthic reef communities globally. Such phase shifts likely have major consequences for ecosystem functions; yet, related knowledge is scarce in general, but particularly at the community level, under ‘in situ’ conditions, and under the influence of changing environmental variables. Thus, we conducted a series of interconnected in situ experiments in coral- and algae-dominated reef communities in the central Red Sea, combining traditional community ecology approaches with novel metabolic and biogeochemical assessments from December 2016 to January 2018. Specifically, we (i) examined the influence of coral-algal phase shifts on recruitment and succession patterns, (ii) assessed the role of benthic pioneer communities in reef carbon and nitrogen dynamics, (iii) developed a novel approach to measure functions of structurally complex reef communities in situ, and (iv) quantified biogeochemical functions of mature coral- and algae-dominated reef communities. The findings suggest that coral-algal phase shifts fundamentally modify critical reef functions at different levels of biological organization, namely from pioneer to mature reef communities. For example, community shifts, through a lower habitat complexity and grazing pressure, decreased the number of coral recruits by >50 %, thereby inhibiting the replenishment of adult coral populations. At the same time, a 30 % higher productivity (annual mean) and increased organic carbon retention in algae-dominated communities supported a fast biomass accumulation and community growth, altering the habitat-specific community metabolism and reef biogeochemistry. Seasonal warming amplified these functional differences between coral- and algae-dominated communities, likely promoting a positive feedback loop of reef degradation under predicted ocean warming. Overall, this dissertation provides quantitative data on critical functions of classical and phase shifted novel reef communities, on tipping points for the collapse of community functions, and potential future winners and losers. The knowledge gained with this thesis helps, thereby, to understand how phase-shifted reef ecosystems function and which services will be generated in comparison to coral-dominated reefs under near-future stress scenarios.

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.

Coral reefs are suffering unprecedented declines in coral cover and species diversity. These changes are often associated with  substantial shifts in community structure to new dominant organisms. Ultimately, these “phase shifts” can be persistent and very difficult to return from. Building insurance against degradation and decreasing the likelihood of reefs undergoing shifts to undesirable states will require sustainable management practices that uphold coral reef resilience. This thesis consists of five papers that contribute new knowledge useful for managing the resilience of coral reefs, and other marine ecosystems. Paper I shows how the morphology of natural substrate (dead coral colonies) can significantly influence coral recruitment patterns. Paper II focuses on larval lipid levels, a key determinant of coral dispersal potential, in a common Caribbean coral (Favia fragum). It shows that i) lipid levels exhibit a significant, non-linear reduction throughout the larval release period of F. fragum and ii) exposure to a common pollutant (copper) could potentially lead to a more rapid lipid consumption in the larvae. Paper III presents a broader analysis of the different undesirable states a coral reef can shift to as a consequence of reef degradation. It concludes that different states are caused by different driving factors and that management must explicitly acknowledge this. Paper IV proposes a suite of resilience indicators that can help managers assess when a coral-dominated reef might be moving towards a shift to an undesirable state. These indicators capture key-processes occuring on different temporal and spatial scales and signal resilience loss early enough for managers to take appropriate measures. Finally, Paper V reviews the feedback loops that reinforce the undesirable states of five important marine ecosystems and suggests certain strategies that can ease the restoration back to healthier conditions. Managing these critical feedbacks will recquire monitoring the processes underpinning these feedbacks, breaking already established feedbacks loops through large-scale management trials and acknowledging transdisciplinary solutions that move management beyond the discipline of ecology / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 5: In progress.

Herbivorous reef fish are a key functional group for the ecological resilience of coral reefs. Asthey feed on algae, a major resource competitor of coral polyps, they can prevent and reversecoral-macroalgal phase shifts. The resilience of the reefs against such phase shifts is given bythe ability of herbivores to keep the system in a cropped state from filamentous algae or bytheir capacity to feed on macroalgae. Most of the management plans that aim to protect coralreefs have been focusing on the establishment of marine protected areas or no-take areas wherefishing activities are strictly restricted or prohibited. In low-income countries, such managedareas can be difficult to accept from a fisher´s perspective and lack of money also tends to leadto limited surveillance capabilities and lowered compliance. These challenges are important toaddress when managing small-scale fisheries and where fish are considered as both, amarketable commodity and a subsistence good.A perhaps less contentious strategy for fishers is gear-based management, where the use offishing gears that are detrimental to coral reef resilience are restricted and at the same timegears that do not compromise resilience are promoted. This study aims to investigate how ninedifferent fishing gears (i.e. different lines, traps, nets and spears) used in the coral reef fisheriesof Zanzibar (Tanzania) capture herbivorous reef fish that can prevent (preventers) or reverse(reversers) coral-macroalgal phase shifts. Two interesting findings emerged from the study.First, different fishing gears had different impacts on these two functional groups where lines,large traps and seine nets fisheries had most impacts. Second, there were monsoonaldifferences in the catch of preventers and reversers. These findings are discussed in relation toi) similar studies conducted in different reef environments and ii) the feasibility of gear-basedmanagement in Zanzibar.

In this thesis, an evaluation of the existing control system for ABB: s HVDC Classic Links is performed in order to investigate whether a possible improvement to commutation failure prediction is possible and to be recommended. The thesis starts with a theoretical approach to the complexity of consequences of increasing the extinction angle (γ) in order to prevent commutation failure in inverter operation, which is later confirmed through using the simulation software PSCAD to evaluate coherence between simulation results and theory. Dynamic power studies are performed through simulations in the electromagnetic time domain transient tool PSCAD in order to establish a possible improvement to the existing commutation failure prediction today used in ABB control systems for HVDC applications.

The connection between phase shifts and the ANC has been explored in the frame of the effective range theory. The main result is that, in practice and under rather simple requirements, scattering states (phases shifts) can be correctly described and connected with bound states via the effective range function, and therefore, ANCs can be accurately determined thanks to the analytic properties of this function. This result has an important impact in stellar evolution due to the ANC and phases shifts are directly connected with capture cross sections which, for instance, determine partially the stage and evolution of stars.<p><p>As a first step, the effective range function is approximated via the effective range expansion which shows that a successful phase-shift description depends on how precise the effective range parameters are determined. Thus, a technique to compute accurately these parameters is developed here. Its construction is based on a set of recurrence relations at low energy, that allows a compact and general description of the truncated<p>effective range expansion. Several potential models are used to illustrate the effectiveness<p>of this technique and to discuss its numerical limitations. The results shows that a very good precision of the effective-range parameters can be achieved; nevertheless, to describe experimental phase shifts several effective-range parameters can be needed, which shows a limitation for practical applications.<p><p>As a second step, the effective range function is analyzed theoretically in an arbitrary energy range. This analysis shows that this function can be decomposed in such a way that contributions of bound states, resonances and background can be separated in a similar way as in the phenomenological R-matrix. In this new form experimental data can be better fitted because the free parameter space is reduced considerably,<p>and therefore, extrapolations are better handled. By construction, the method agrees with the scattering matrix properties which allows a simple calculation of resonances (locations and widths) and asymptotic normalization constants (ANCs). Several tests are successfully performed via potential models. Phase shifts for the 2 + partial wave of the 12C+α are analyzed with this method. They are correctly described including both<p>resonances at Ec.m. = 2.7 and 4.4 MeV. For the 6.92 MeV (2+) exited state of 16O, the ANC estimation 112(8) × 10 3 fm^−1/2 is obtained taking into account statistical errors. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Situé dans le noyau suprachiasmatique (SCN) de l’hypothalamus, l'horloge principale contrôle les rythmes des processus comportementaux et métaboliques chez les mammifères. Par exemple, les rythmes quotidiens de veille-sommeil, d'alimentation-jeûne, de glycémie, de tolérance au glucose et de sensibilité à l'insuline sont régulés par l'horloge SCN. La lumière est le synchroniseur principal du SCN, même si de nombreux facteurs autres que la lumière, tels que l'éveil comportemental ou des facteurs métaboliques, peuvent également moduler la phase ou la période des SCN. L'objectif de cette thèse était d'étudier différents aspects des interactions entre l'éveil comportemental, les rythmes circadiens et le métabolisme du glucose. Dans la première partie, nous avons déterminé l'action centrale du Gastrin-Releasing Peptide (GRP), un neuropeptide synthétisé dans le SCN, sur le métabolisme du glucose. Nos résultats indiquent qu’une injection icv de GRP induit une hyperglycémie prolongée. Nous avons également montré qu’une privation de sommeil à court terme conduit à une détérioration de la tolérance au glucose. Dans la deuxième partie, nous avons démontré que l'éveil comportemental induit par la privation de sommeil ou une injection de caféine améliore l’entraînement photique de l'horloge SCN chez un rongeur diurne : le rat roussard du Soudan, Arvicanthis ansorgei. Ces réponses circadiennes chez une espèce diurne qui sont opposées à celles précédemment mises en évidence chez les rongeurs nocturnes pourraient avoir des applications biomédicales. / Located in the hypothalamic suprachiasmatic nucleus (SCN), the master clock generates rhythms of behavioural and metabolic processes in mammals. For example, daily rhythms of sleep-wake, fasting-feeding, plasma glucose concentration, glucose tolerance and insulin sensitivity are regulated by the SCN clock. Light is the primary synchronizer of SCN pacemaker though many light-independent factors such as behavioural arousal and metabolic cues also have phase and period resetting properties. The aim of thesis was to study different aspects of the interactions between behavioural arousal, circadian rhythms and glucose metabolism. In the first part, we extended the study of brain control of glucose metabolism by investigating the central action of gastrin-releasing peptide (GRP), a neuropeptide synthesized in the SCN, on glucose metabolism. Our result indicates that central GRP induces long-lasting hyperglycemia. We also showed that acute sleep deprivation leads to impaired glucose tolerance. In the second part, we demonstrated that behavioural arousal induced by sleep deprivation or caffeine treatment enhances photic-entrainment of the SCN clock in the diurnal Sudanian grass rat, Arvicanthis ansorgei. These circadian responses in a diurnal species are opposite to the earlier findings in nocturnal rodents and may have biomedical applications.