Exposure modelling to traffic-related air toxic pollutants

Atualmente, a poluição atmosférica constitui uma das principais causas ambientais de mortalidade. Cerca de 30% da população europeia residente em áreas urbanas encontra-se exposta a níveis de poluição atmosférica superiores aos valores- limite de qualidade do ar legislados para proteção da saúde humana, representando o tráfego rodoviário uma das principais fontes de poluição urbana. Além dos poluentes tradicionais avaliados em áreas urbanas, os poluentes classificados como perigosos para a saúde (Hazard Air Pollutants - HAPs) têm particular relevância devido aos seus conhecidos efeitos tóxicos e cancerígenos. Neste sentido, a avaliação da exposição tornase primordial para a determinação da relação entre a poluição atmosférica urbana e efeitos na saúde. O presente estudo tem como principal objetivo o desenvolvimento e implementação de uma metodologia para avaliação da exposição individual à poluição atmosférica urbana relacionada com o tráfego rodoviário. De modo a atingir este objetivo, foram identificados os parâmetros relevantes para a quantificação de exposição e analisados os atuais e futuros potenciais impactos na saúde associados com a exposição à poluição urbana. Neste âmbito, o modelo ExPOSITION (EXPOSure model to traffIc-relaTed aIr pOllutioN) foi desenvolvido baseado numa abordagem inovadora que envolve a análise da trajetória dos indivíduos recolhidas por telemóveis com tecnologia GPS e processadas através da abordagem de data mining e análise geoespacial. O modelo ExPOSITION considera também uma abordagem probabilística para caracterizar a variabilidade dos parâmetros microambientais e a sua contribuição para exposição individual. Adicionalmente, de forma a atingir os objetivos do estudo foi desenvolvido um novo módulo de cálculo de emissões de HAPs provenientes do transporte rodoviário. Neste estudo, um sistema de modelação, incluindo os modelos de transporteemissões- dispersão-exposição, foi aplicado na área urbana de Leiria para quantificação de exposição individual a PM2.5 e benzeno. Os resultados de modelação foram validados com base em medições obtidas por monitorização pessoal e monitorização biológica verificando-se uma boa concordância entre os resultados do modelo e dados de medições. A metodologia desenvolvida e implementada no âmbito deste trabalho permite analisar e estimar a magnitude, frequência e inter e intra-variabilidade dos níveis de exposição individual, bem como a contribuição de diferentes microambientes, considerando claramente a sequência de eventos de exposição e relação fonte-recetor, que é fundamental para avaliação dos efeitos na saúde e estudos epidemiológicos. O presente trabalho contribui para uma melhor compreensão da exposição individual em áreas urbanas, proporcionando novas perspetivas sobre a exposição individual, essenciais na seleção de estratégias de redução da exposição à poluição atmosférica urbana, e consequentes efeitos na saúde.

Integrated Bayesian network frameworks for modelling complex ecological issues

Ecological problems are typically multi faceted and need to be addressed from a scientific and a management perspective. There is a wealth of modelling and simulation software available, each designed to address a particular aspect of the issue of concern. Choosing the appropriate tool, making sense of the disparate outputs, and taking decisions when little or no empirical data is available, are everyday challenges facing the ecologist and environmental manager. Bayesian Networks provide a statistical modelling framework that enables analysis and integration of information in its own right as well as integration of a variety of models addressing different aspects of a common overall problem. There has been increased interest in the use of BNs to model environmental systems and issues of concern. However, the development of more sophisticated BNs, utilising dynamic and object oriented (OO) features, is still at the frontier of ecological research. Such features are particularly appealing in an ecological context, since the underlying facts are often spatial and temporal in nature. This thesis focuses on an integrated BN approach which facilitates OO modelling. Our research devises a new heuristic method, the Iterative Bayesian Network Development Cycle (IBNDC), for the development of BN models within a multi-field and multi-expert context. Expert elicitation is a popular method used to quantify BNs when data is sparse, but expert knowledge is abundant. The resulting BNs need to be substantiated and validated taking this uncertainty into account. Our research demonstrates the application of the IBNDC approach to support these aspects of BN modelling. The complex nature of environmental issues makes them ideal case studies for the proposed integrated approach to modelling. Moreover, they lend themselves to a series of integrated sub-networks describing different scientific components, combining scientific and management perspectives, or pooling similar contributions developed in different locations by different research groups. In southern Africa the two largest free-ranging cheetah (Acinonyx jubatus) populations are in Namibia and Botswana, where the majority of cheetahs are located outside protected areas. Consequently, cheetah conservation in these two countries is focussed primarily on the free-ranging populations as well as the mitigation of conflict between humans and cheetahs. In contrast, in neighbouring South Africa, the majority of cheetahs are found in fenced reserves. Nonetheless, conflict between humans and cheetahs remains an issue here. Conservation effort in South Africa is also focussed on managing the geographically isolated cheetah populations as one large meta-population. Relocation is one option among a suite of tools used to resolve human-cheetah conflict in southern Africa. Successfully relocating captured problem cheetahs, and maintaining a viable free-ranging cheetah population, are two environmental issues in cheetah conservation forming the first case study in this thesis. The second case study involves the initiation of blooms of Lyngbya majuscula, a blue-green algae, in Deception Bay, Australia. L. majuscula is a toxic algal bloom which has severe health, ecological and economic impacts on the community located in the vicinity of this algal bloom. Deception Bay is an important tourist destination with its proximity to Brisbane, Australia’s third largest city. Lyngbya is one of several algae considered to be a Harmful Algal Bloom (HAB). This group of algae includes other widespread blooms such as red tides. The occurrence of Lyngbya blooms is not a local phenomenon, but blooms of this toxic weed occur in coastal waters worldwide. With the increase in frequency and extent of these HAB blooms, it is important to gain a better understanding of the underlying factors contributing to the initiation and sustenance of these blooms. This knowledge will contribute to better management practices and the identification of those management actions which could prevent or diminish the severity of these blooms.

Removal of toxic metals in a multi metal system using sorbents for potential application to urban stormwater treatment

In the context of increasing demand for potable water and the depletion of water resources, stormwater is a logical alternative. However, stormwater contains pollutants, among which metals are of particular interest due to their toxicity and persistence in the environment. Hence, it is imperative to remove toxic metals in stormwater to the levels prescribed by drinking water guidelines for potable use. Consequently, various techniques have been proposed, among which sorption using low cost sorbents is economically viable and environmentally benign in comparison to other techniques. However, sorbents show affinity towards certain toxic metals, which results in poor removal of other toxic metals. It was hypothesised in this study that a mixture of sorbents that have different metal affinity patterns can be used for the efficient removal of a range of toxic metals commonly found in stormwater. The performance of six sorbents in the sorption of Al, Cr, Cu, Pb, Ni, Zn and Cd, which are the toxic metals commonly found in urban stormwater, was investigated to select suitable sorbents for creating the mixtures. For this purpose, a multi criteria analytical protocol was developed using the decision making methods: PROMETHEE (Preference Ranking Organisation METHod for Enrichment Evaluations) and GAIA (Graphical Analysis for Interactive Assistance). Zeolite and seaweed were selected for the creation of trial mixtures based on their metal affinity pattern and the performance on predetermined selection criteria. The metal sorption mechanisms employed by seaweed and zeolite were defined using kinetics, isotherm and thermodynamics parameters, which were determined using the batch sorption experiments. Additionally, the kinetics rate-limiting steps were identified using an innovative approach using GAIA and Spearman correlation techniques developed as part of the study, to overcome the limitation in conventional graphical methods in predicting the degree of contribution of each kinetics step in limiting the overall metal removal rate. The sorption kinetics of zeolite was found to be primarily limited by intraparticle diffusion followed by the sorption reaction steps, which were governed mainly by the hydrated ionic diameter of metals. The isotherm study indicated that the metal sorption mechanism of zeolite was primarily of a physical nature. The thermodynamics study confirmed that the energetically favourable nature of sorption increased in the order of Zn < Cu < Cd < Ni < Pb < Cr < Al, which is in agreement with metal sorption affinity of zeolite. Hence, sorption thermodynamics has an influence on the metal sorption affinity of zeolite. On the other hand, the primary kinetics rate-limiting step of seaweed was the sorption reaction process followed by intraparticle diffusion. The boundary layer diffusion was also found to limit the metal sorption kinetics at low concentration. According to the sorption isotherm study, Cd, Pb, Cr and Al were sorbed by seaweed via ion exchange, whilst sorption of Ni occurred via physisorption. Furthermore, ionic bonding is responsible for the sorption of Zn. The thermodynamics study confirmed that sorption by seaweed was energetically favourable in the order of Zn < Cu < Cd < Cr . Al < Pb < Ni. However, this did not agree with the affinity series derived for seaweed suggesting a limited influence of sorption thermodynamics on metal affinity for seaweed. The investigation of zeolite-seaweed mixtures indicated that mixing sorbents have an effect on the kinetics rates and the sorption affinity. Additionally, the theoretical relationships were derived to predict the boundary layer diffusion rate, intraparticle diffusion rate, the sorption reaction rate and the enthalpy of mixtures based on that of individual sorbents. In general, low coefficient of determination (R2) for the relationships between theoretical and experimental data indicated that the relationships were not statistically significant. This was attributed to the heterogeneity of the properties of sorbents. Nevertheless, in relative terms, the intraparticle diffusion rate, sorption reaction rate and enthalpy of sorption had higher R2 values than the boundary layer diffusion rate suggesting that there was some relationship between the former set of parameters of mixtures and that of sorbents. The mixture, which contained 80% of zeolite and 20% of seaweed, showed similar affinity for the sorption of Cu, Ni, Cd, Cr and Al, which was attributed to approximately similar sorption enthalpy of the metal ions. Therefore, it was concluded that the seaweed-zeolite mixture can be used to obtain the same affinity for various metals present in a multi metal system provided the metal ions have similar enthalpy during sorption by the mixture.

Mapping, monitoring, and modelling of hazardous waste sites

Management of the industrial nations' hazardous waste is a current and exponentially increasing, global threatening situation. Improved environmental information must be obtained and managed concerning the current status, temporal dynamics and potential future status of these critical sites. To test the application of spatial environmental techniques to the problem of hazardous waste sites, as Superfund (CERCLA) test site was chosen in an industrial/urban valley experiencing severe TCE, PCE, and CTC ground water contamination. A paradigm is presented for investigating spatial/environmental tools available for the mapping, monitoring and modelling of the environment and its toxic contaminated plumes. This model incorporates a range of technical issues concerning the collection of data as augmented by remotely sensed tools, the format and storage of data utilizing geographic information systems, and the analysis and modelling of environment through the use of advance GIS analysis algorithms and geophysic models of hydrologic transport including statistical surface generation. This spatial based approach is evaluated against the current government/industry standards of operations. Advantages and lessons learned of the spatial approach are discussed.

Human health risk of toxic chemical pollutants generated from traffic and land use activities

The research project developed a quantitative approach to assess the risk to human health from heavy metals and polycyclic aromatic hydrocarbons in urban stormwater based on traffic and land use factors. The research outcomes are expected to strengthen the scientifically robust management and reuse of urban stormwater. The innovative methodology developed can be applied to evaluate human health risk in relation to toxic chemical pollutants in urban stormwater runoff and for the development of effective risk mitigation strategies.

Build-up of toxic metals on the impervious surfaces of a commercial seaport

In the context of increasing threats to the sensitive marine ecosystem by toxic metals, this study investigated the metal build-up on impervious surfaces specific to commercial seaports. The knowledge generated in this study will contribute to managing toxic metal pollution of the marine ecosystem. The study found that inter-modal operations and main access roadway had the highest loads followed by container storage and vehicle marshalling sites, while the quay line and short term storage areas had the lowest. Additionally, it was found that Cr, Al, Pb, Cu and Zn were predominantly attached to solids, while significant amount of Cu, Pb and Zn were found as nutrient complexes. As such, treatment options based on solids retention can be effective for some metal species, while ineffective for other species. Furthermore, Cu and Zn are more likely to become bioavailable in seawater due to their strong association with nutrients. Mathematical models to replicate the metal build-up process were also developed using experimental design approach and partial least square regression. The models for Cr and Pb were found to be reliable, while those for Al, Zn and Cu were relatively less reliable, but could be employed for preliminary investigations.

Osmotic stress does not trigger brevetoxin production in the dinoflagellate Karenia brevis

With the global proliferation of toxic Harmful Algal Bloom (HAB) species, there is a need to identify the environmental and biological factors that regulate toxin production. One such species, Karenia brevis, forms nearly annual blooms that threaten coastal regions throughout the Gulf of Mexico. This dinoflagellate produces brevetoxins, potent neurotoxins that cause neurotoxic shellfish poisoning and respiratory illness in humans, as well as massive fish kills. A recent publication reported that a rapid decrease in salinity increased cellular toxin quotas in K. brevis and hypothesized that brevetoxins serve a role in osmoregulation. This finding implied that salinity shifts could significantly alter the toxic impacts of blooms. We repeated the original experiments separately in three different laboratories and found no evidence for increased brevetoxin production in response to low-salinity stress in any of the eight K. brevis strains we tested, including three used in the original study. Thus, we find no support for an osmoregulatory function of brevetoxins. The original publication also stated that there was no known cellular function for brevetoxins. However, there is increasing evidence that brevetoxins promote survival of the dinoflagellates by deterring grazing by zooplankton. Whether they have other as yet unidentified cellular functions is currently unknown.

Experimental study on the impact of dinoflagellate Alexandrium species on populations of the rotifer Brachionus plicatilis

To investigate harmful effects of the dinoflagellate Alexandrium species on microzooplankton, the rotifer Brachionus plicatilis was chosen as an assay species, and tested with 10 strains of Alexandrium including one known non-PSP-producer (Alexandrium tamarense, AT-6). HPLC analysis confirmed the PSP-content of the various strains: Alexandrium lusitanicum, Alexandrium minutum and Alexandrium tamarense (ATHK, AT5-1, AT5-3, ATC102, ATC103) used in the experiment were PSP-producers. No PSP toxins were detected in the strains Alexandrium sp1, Alexandrium sp2. Exposing rotifer populations to the densities of 2000 cells ml(-1) of each of these 10 Alexandrium strains revealed that the (non-PSP) A. tarnarense (AT-6) and two other PSP-producing algae: A. lusitanicum, A. minutum, did not appear to adversely impact rotifer populations. Rotifers exposed to these three strains were able to maintain their population numbers, and in some cases, increase them. Although some increases in rotifer population growth following exposures to these three algal species were noted, the rate was less than for the non-exposed control rotifer groups. In contrast, the remaining seven algal strains (A. tamarense ATHK, AT5-1, AT5-3, ATC102, ATC103; also Alexandrium sp1 and Alexandrium sp2) all have adverse effects on the rotifers. Dosing rotifers with respective algal cell densities of 2000 cells ml-1 each, for Alexandrium spl, Alexandrium sp2, and A. tamarense strains ATHK and ATC103 showed mean lethal time (LT50) on rotifer populations of 21, 28, 29, and 36h, respectively. The remaining three species (A. tamarense strains AT5-1, AT5-3, ATC102) caused respective mean rotifer LT50S of 56, 56, and 71 h, compared to 160 h for the unexposed "starved control" rotifers. Experiments to determine ingestion rates for the rotifers, based on changes in their Chlorophyll a content, showed that the rotifers could feed on A. lusitanicum, A. minutum and A. tamarense strain AT-6, but could graze to little or no extent upon algal cells of the other seven strains. The effects on rotifers exposed to different cell densities, fractions, and growth phases of A. tamarense algal culture were respectively compared. It was found that only the whole algal cells had lethal effects, with strongest impact being shown by the early exponential growth phase of A. tamarense. The results indicate that some toxic mechanism(s), other than PSP and present in whole algal cells, might be responsible for the adverse effects on the exposed rotifers. (C) 2004 Elsevier B.V. All rights reserved.

Effects of the dinoflagellate Alexandrium tamarense on early development of the scallop Argopecten irradians concentricus

The effects of Alexandrium tamarense (strain ATHK) on early development of the bay scallop Argopecten irradians concentricus were studied under laboratory conditions. The algal culture was verified by HPLC to produce paralytic shellfish poisoning (PSP) at a level of 37.48 fmol/cell. Survival of the scallop larvae was not affected when they were grown with A. tamarense at concentrations of 500-10,000 cells/ml for 48 h. However, the activity of D-shape larvae was inhibited after 48-h exposure to A. tamarense at the algal cell density of 10,000 cells/ml. Scallop growth was inhibited significantly by A. tantarense during a 14-day exposure starting at the eye-spot larval stage. The size of juvenile scallops in the group of 10,000 cells/ml was only about 32% of that of the controls, although no obvious effect of A. tamarense was found on the rate of larval metamorphosis. All juvenile scallops survived in algal concentrations of 600-2400 cells/ml, however, attachment rates were significantly lower than control values after a 5-h exposure to A. tamarense at concentrations >600 cells/ml, while they were not obviously reduced after only 1 h of exposure. At concentrations >600 cells/ml, the climbing ability of juveniles was clearly reduced by exposure to A. tamarense after only 1 h. The climbing rate and height were only 55% and 45%, respectively, of those of the controls, when exposed to A. tantarense at a concentration of 600 cells/ml. The results indicated that A. tamarense blooms may have detrimental impacts on shellfish at early life stages, therefore, special attention should be paid to the toxic algal blooms in shellfish breeding area. (C) 2003 Elsevier Science B.V. All rights reserved.

Inhibition of egg hatching success and larvae survival of the scallop, Chlamys farreri, associated with exposure to cells and cell fragments of the dinoflagellate Alexandrium tamarense

We report an apparently novel toxic effect of the dinoflagellate Alexandrium tamarense, manifested by inhibition of the egg hatching success of the scallop, Chlamys farreri. The hatching rate of C. farreri approached only 30% of controls when its fertilised eggs were exposed for 36 h to A. tamarense cells or cellular fragments at a concentration of 100 cells/ml, and the hatching rate was just 5% after exposure to A. tamarense of 500 cells/ml. Similar exposures of the fertilised scallop eggs to two other algal species, the diatom Phaeodactylum tricornutum and the raphidophyte Heterosigma carterae, resulted in no such toxicity or inhibitory effects.. Likewise, exposure of eggs to standard STX toxin. as well as to A. tamarense cell contents (supernant of re-suspended algal cells following ultrasonication and centrifugation), did not elicit this inhibitory response. However, exposure of the scallop eggs to cell cultures, intact algal cells, or cell fragments of A. tamarense produced marked toxicity. The alga also influenced larvae at early D-shape stage of scallop. The survival rates began to decrease significantly after exposed for 6 days at concentration of 3000 cells/ml and above: no larvae could survive after 14-day exposure to A. tamarense at 10,000 cells/ml or 20-day at 5000 cells/ml. The results indicated the production of novel substances from A. tamarense which can cause adverse effects on egg hatching and survival of the scallop larvae, The experiment also found that the developmental stages before blastula was the developmental period most sensitive to the A. tamarense toxin(s) and the alga at early exponential stage had the strongest effect on egg hatching comparing with other growth phases. The adverse effect of A. tamarense on early development of scallops may cause decline of shellfish population and may have further impact on marine ecosystem. (C) 2001 Elsevier Science Ltd. All rights reserved.

Computer modelling of human behaviour in aircraft fire accidents

The mathematical simulation of the evacuation process has a wide and largely untapped scope of application within the aircraft industry. The function of the mathematical model is to provide insight into complex behaviour by allowing designers, legislators, and investigators to ask ‘what if’ questions. Such a model, EXODUS, is currently under development, and this paper describes its evolution and potential applications. EXODUS is an egress model designed to simulate the evacuation of large numbers of individuals from an enclosure, such as an aircraft. The model tracks the trajectory of each individual as they make their way out of the enclosure or are overcome by fire hazards, such as heat and toxic gases. The software is expert system-based, the progressive motion and behaviour of each individual being determined by a set of heuristics or rules. EXODUS comprises five core interacting components: (i) the Movement Submodel — controls the physical movement of individual passengers from their current position to the most suitable neighbouring location; (ii) the Behaviour Submodel — determines an individual's response to the current prevailing situation; (iii) the Passenger Submodel — describes an individual as a collection of 22 defining attributes and variables; (iv) the Hazard Submodel — controls the atmospheric and physical environment; and (v) the Toxicity Submodel — determines the effects on an individual exposed to the fire products, heat, and narcotic gases through the Fractional Effective Dose calculations. These components are briefly described and their capabilities and limitations are demonstrated through comparison with experimental data and several hypothetical evacuation scenarios.

Modelling the combined impacts of climate change and direct anthropogenic drivers on the ecosystem of the northwest European continental shelf

The potential response of the marine ecosystem of the northwest European continental shelf to climate change under a medium emissions scenario (SRES A1B) is investigated using the coupled hydrodynamics-ecosystem model POLCOMS-ERSEM. Changes in the near future (2030–2040) and the far future (2082–2099) are compared to the recent past (1983–2000). The sensitivity of the ecosystem to potential changes in multiple anthropogenic drivers (river nutrient loads and benthic trawling) in the near future is compared to the impact of changes in climate. With the exception of the biomass of benthic organisms, the influence of the anthropogenic drivers only exceeds the impact of climate change in coastal regions. Increasing river nitrogen loads has a limited impact on the ecosystem whilst reducing river nitrogen and phosphate concentrations affects net primary production(netPP) and phytoplankton and zooplankton biomass. Direct anthropogenic forcing is seen to mitigate/amplify the effects of climate change. Increasing river nitrogen has the potential to amplify the effects of climate change at the coast by increasing netPP. Reducing river nitrogen and phosphate mitigates the effects of climate change for netPP and the biomass of small phytoplankton and large zooplankton species but amplifies changes in the biomass of large phytoplankton and small zooplankton.

Physical and immunoaffinity extraction of paralytic shellfish poisoning toxins from cultures of the dinoflagellate Alexandrium tamarense

In the present study the extraction of paralytic shellfish poisoning (PSP) toxins from a toxic strain of the marine dinoflagellate Alexandrium tamarense CCMP-1493 using various mechanical and/or physical procedures was investigated. PBS buffer was investigated as the extraction solvent in order for these procedures to be used directly with immuno-magnetic Ferrospheres-N. The extraction was performed following the determination of when toxin content by the algae was at its highest during batch culture. The methods used for cell lysis and toxin extraction included freeze-thawing, freeze-boiling, steel ball bearing beating, glass bead beating, and sonication. The steel ball bearing beating was determined to release a similar amount of toxin when compared to a modified standard extraction method which was reported to release 100% of toxins from the algal cells and was therefore used in the next phase of the study. This next phase was to determine the feasibility of utilising an antibody coupled to novel magnetic microspheres (Ferrospheres-N) as a simple, rapid immune-capture procedure for PSP toxins extracted from the algae. The effects of increasing mass of Ferrospheres-N on the immuno-capture of the PSP toxins from the toxic algal strain extracts were investigated. Toxin recovery was found to increase when an increasing mass of Ferrospheres-N was used until 96.2% (+/- 1.3 SD) of the toxin extracted from the cells was captured and eluted. Toxin recovery was determined by comparison to an appropriate PSP toxin standard curve following analysis by the AOAC HPLC method. (C) 2011 Elsevier B.V. All rights reserved.

Multiple linear and principal component regressions for modelling ecotoxicity bioassay response

The ecotoxicological response of the living organisms in an aquatic system depends on the physical, chemical and bacteriological variables, as well as the interactions between them. An important challenge to scientists is to understand the interaction and behaviour of factors involved in a multidimensional process such as the ecotoxicological response.With this aim, multiple linear regression (MLR) and principal component regression were applied to the ecotoxicity bioassay response of Chlorella vulgaris and Vibrio fischeri in water collected at seven sites of Leça river during five monitoring campaigns (February, May, June, August and September of 2006). The river water characterization included the analysis of 22 physicochemical and 3 microbiological parameters. The model that best fitted the data was MLR, which shows: (i) a negative correlation with dissolved organic carbon, zinc and manganese, and a positive one with turbidity and arsenic, regarding C. vulgaris toxic response; (ii) a negative correlation with conductivity and turbidity and a positive one with phosphorus, hardness, iron, mercury, arsenic and faecal coliforms, concerning V. fischeri toxic response. This integrated assessment may allow the evaluation of the effect of future pollution abatement measures over the water quality of Leça River.

Regulation of gene expression in the dinoflagellate Lingulodinium polyedrum

Les dinoflagellés sont des eucaryotes unicellulaires que l’on retrouve autant en eau douce qu’en milieu marin. Ils sont particulièrement connus pour causer des fleurs d’algues toxiques nommées ‘marée-rouge’, ainsi que pour leur symbiose avec les coraux et pour leur importante contribution à la fixation du carbone dans les océans. Au point de vue moléculaire, ils sont aussi connus pour leur caractéristiques nucléaires uniques, car on retrouve généralement une quantité immense d’ADN dans leurs chromosomes et ceux-ci sont empaquetés et condensés sous une forme cristalline liquide au lieu de nucléosomes. Les gènes encodés par le noyau sont souvent présents en multiples copies et arrangés en tandem et aucun élément de régulation transcriptionnelle, y compris la boite TATA, n’a encore été observé. L’organisation unique de la chromatine des dinoflagellés suggère que différentes stratégies sont nécessaires pour contrôler l’expression des gènes de ces organismes. Dans cette étude, j’ai abordé ce problème en utilisant le dinoflagellé photosynthétique Lingulodinium polyedrum comme modèle. L. polyedrum est d’un intérêt particulier, car il a plusieurs rythmes circadiens (journalier). À ce jour, toutes les études sur l’expression des gènes lors des changements circadiens ont démontrées une régulation à un niveau traductionnel. Pour mes recherches, j’ai utilisé les approches transcriptomique, protéomique et phosphoprotéomique ainsi que des études biochimiques pour donner un aperçu de la mécanique de la régulation des gènes des dinoflagellés, ceci en mettant l’accent sur l’importance de la phosphorylation du système circadien de L. polyedrum. L’absence des protéines histones et des nucléosomes est une particularité des dinoflagellés. En utilisant la technologie RNA-Seq, j’ai trouvé des séquences complètes encodant des histones et des enzymes modifiant les histones. L polyedrum exprime donc des séquences conservées codantes pour les histones, mais le niveau d’expression protéique est plus faible que les limites de détection par immunodétection de type Western. Les données de séquençage RNA-Seq ont également été utilisées pour générer un transcriptome, qui est une liste des gènes exprimés par L. polyedrum. Une recherche par homologie de séquences a d’abord été effectuée pour classifier les transcrits en diverses catégories (Gene Ontology; GO). Cette analyse a révélé une faible abondance des facteurs de transcription et une surprenante prédominance, parmi ceux-ci, des séquences à domaine Cold Shock. Chez L. polyedrum, plusieurs gènes sont répétés en tandem. Un alignement des séquences obtenues par RNA-Seq avec les copies génomiques de gènes organisés en tandem a été réalisé pour examiner la présence de transcrits polycistroniques, une hypothèse formulée pour expliquer le manque d’élément promoteur dans la région intergénique de la séquence de ces gènes. Cette analyse a également démontré une très haute conservation des séquences codantes des gènes organisés en tandem. Le transcriptome a également été utilisé pour aider à l’identification de protéines après leur séquençage par spectrométrie de masse, et une fraction enrichie en phosphoprotéines a été déterminée comme particulièrement bien adapté aux approches d’analyse à haut débit. La comparaison des phosphoprotéomes provenant de deux périodes différentes de la journée a révélée qu’une grande partie des protéines pour lesquelles l’état de phosphorylation varie avec le temps est reliées aux catégories de liaison à l’ARN et de la traduction. Le transcriptome a aussi été utilisé pour définir le spectre des kinases présentes chez L. polyedrum, qui a ensuite été utilisé pour classifier les différents peptides phosphorylés qui sont potentiellement les cibles de ces kinases. Plusieurs peptides identifiés comme étant phosphorylés par la Casein Kinase 2 (CK2), une kinase connue pour être impliquée dans l’horloge circadienne des eucaryotes, proviennent de diverses protéines de liaison à l’ARN. Pour évaluer la possibilité que quelques-unes des multiples protéines à domaine Cold Shock identifiées dans le transcriptome puissent moduler l’expression des gènes de L. polyedrum, tel qu’observé chez plusieurs autres systèmes procaryotiques et eucaryotiques, la réponse des cellules à des températures froides a été examinée. Les températures froides ont permis d’induire rapidement un enkystement, condition dans laquelle ces cellules deviennent métaboliquement inactives afin de résister aux conditions environnementales défavorables. Les changements dans le profil des phosphoprotéines seraient le facteur majeur causant la formation de kystes. Les phosphosites prédits pour être phosphorylés par la CK2 sont la classe la plus fortement réduite dans les kystes, une découverte intéressante, car le rythme de la bioluminescence confirme que l’horloge a été arrêtée dans le kyste.