Thesis advisor: Gabor T. Marth / To help improve the analysis of forward genetic screens, we have developed an efficient and automated pipeline for mutational profiling using our reference guided tools including MOSAIK and FREEBAYES. Studies using next generation sequencing technologies currently employ either reference guided alignment or de novo assembly to analyze the massive amount of short read data produced by second generation sequencing technologies; the far more common approach being reference guided alignment due to the massive computational and sequencing costs associated with de novo assembly. The success of reference guided alignment is dependent on three factors; the accuracy of the reference, the ability of the mapper to correctly place a read, and the degree to which a variant allele differs from the reference. Reference assemblies are not perfect and none are entirely complete. Moreover, read mappers can only map reads in genomic locations that are unique enough to confidently place reads; paralogous sections, such as related gene families, cannot be characterized and are often ignored. Further, variant alleles that drastically alter the subject's DNA, such as insertions or deletions (INDELs), will not map to the reference and are either entirely missed or require further downstream analysis to characterize. Most importantly, reference guided methods are restricted to organisms for which such reference genomes have been assembled. The current alternative, de novo assembly of a genome, is prohibitively expensive for most labs requiring deep read coverage from numerous different library preparations as well as massive computing power. To address the shortcomings of current methods, while eliminating the costs intrinsic to de novo sequence assembly, we developed RUFUS, a novel, completely reference-independent variant discovery tool. RUFUS directly compares raw sequence data from two or more samples and identifies groups of reads unique to one or the other sample. RUFUS has at least the same variant detection sensitivity as mapping methods, with greatly increased specificity for SNPs and INDEL variation events. RUFUS is also capable of extremely sensitive copy number detection, without any restriction on event length. By modeling the underlying k-mer distribution, RUFUS produces a specific copy number spectrum for each individual sample. Applying a Bayesian detection method to detect changes in k-mer content between two samples, RUFUS produces copy number calls that are equally as sensitive as traditional copy number detection methods with far fewer false positives. Our data suggest that RUFUS' reference-free approach to variant discovery is able to substantially improve upon existing variant detection methods: reducing reference biases, reducing false positive variants, and detecting copy number variants with excellent sensitivity and specificity. / Thesis (PhD) — Boston College, 2014. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Le manuscrit présente des expériences réalisées avec des gaz quantiques de Chrome, un élément présentant un large spin électronique S=3 et des interactions dipolaires non négligeables. Nous avons produit un nouveau gaz quantique, une mer de Fermi avec l'isotope ⁵³Cr, en optimisant la co-évaporation avec l'isotope bosonique, contenant jusqu’à 1000 atomes a T=TF= 0.66± 0.08. Nous avons obtenu de nouveaux résultats sur la thermodynamique d'un condensat de Bose Einstein (CBE) avec degré de liberté de spin. En refroidissant rapidement un gaz thermique multi-composante, nous observons que la dynamique de condensation est affectée par les collisions d'échange de spin. Nous démontrons aussi un nouveau mécanisme de refroidissement, utilisant le degré de liberté de spin, lorsque le CBE est produit dans le niveau de spin de plus basse énergie. Les interactions dipolaires peuplent thermiquement les états de spin excités à bas champ magnétique, et une purification du CBE est obtenue en retirant sélectivement ces atomes. Enfin nous présentons des expériences de dynamique de spin. Dans une première expérience, cette dynamique est obtenue en utilisant un double puits avec des états de spin opposés. Ceci a permis une première mesure d'une des longueurs de diffusion du ⁵²Cr: ɑo = 13.5 ±¹⁵ ₁₀ aB. Nous présentons également des résultats préliminaires dans un piége harmonique et dans un réseau3D. La dynamique de spin est produite par rotation du spin des atomes. La comparaison avecla théorie nous permet de mettre en évidences l'apparition de corrélations quantiques. / This thesis presents experimental results performed with Quantum gases of Chromium atoms. The specificity of Chromium resides in its large electronic spin S=3 and non negligible dipole-dipole interaction (DDI) between atoms. We produced a new quantum gas, a Fermi sea of the ⁵³Cr isotope. Optimization of the co-evaporation with the ⁵²Cr bosonic isotope leads to 10³ atoms at T=TF= 0.66± 0.08. We obtained new results on thermodynamics of a spinor Bose gas. By "shock cooling" a thermal multi-spin component gas, we find that the dynamics of the BEC is affected by spin changing collisions. We also demonstrate a new cooling mechanism based on the spin degrees of freedom when the Bose Einstein condensate (BEC) is in the lowest energy spin state. Dipolar interactions thermally populate spin excited states at low magnetic field. Purication of the BEC is obtained by selectively removing these thermal atoms. Finally, we present spin dynamics experiments. spin following preparation of atoms in a double well trap in opposite stretch spin states allow to measure the last unknown scattering length of ⁵²Cr: ɑo = 13.5 ±¹⁵ ₁₀ ɑB (with ɑB the Bohr radius). We then present preliminary results performed in a 3D lattice and in the bulk, where spin excitation is performed by a spin rotation. We investigate for different experimental congurations which of a theory with or without quantum correlations ts best our data.

La mer Caspienne qui est devenue l’objet du droit international depuis le XVIIIe siècle n’a jamais connu un statut juridique précis. Cet espace dont la nature aquatique fait l’objet de divergence était dominé par l’URSS jusqu’en 1991. Cependant, à la suite de la disparition de l’URSS, la mer Caspienne - désormais entourée de cinq États riverains (Azerbaïdjan, Iran,Kazakhstan, Russie et Turkménistan) – a fait sa réapparition sur la scène internationale, surtout en raison de ses riches ressources naturelles. C’est précisément dans ces conditions que la question de la situation juridique de la mer Caspienne au regard du droit international s’est posée à la fin du XXe siècle. Il convient donc de former un régime juridique de la mer Caspienne adéquat et durable à long terme et de trouver des solutions pour le règlement desdifférends juridiques entre les États caspiens. / The Caspian Sea which has become the object of international law since the eighteenth century has never had a clear legal status. This space of which the aquatic nature is not defined was dominated by the Soviet Union until 1991. However, following the collapse of the USSR, the Caspian Sea - now surrounded by five littoral States (Azerbaijan, Iran, Kazakhstan, Russia and Turkmenistan) - has re-emerged on the international scene, especially because of its rich natural resources. It is precisely in these circumstances that the question of legal status of the Caspian Sea under international law arose in the late twentieth century. Therefore, it is necessary to form an adequate and sustainable long-term legal regime of theCaspian Sea and to find solutions for the settlement of legal disputes between the Caspian States.

Les phtalates (PAEs) sont un groupe de contaminants organiques émergents qui sont devenus une préoccupation majeure en raison de leur omniprésence dans le milieu marin et de leurs effets perturbateurs sur le système endocrinien. Cependant, leur répartition en Méditerranée est assez mal connue, principalement en raison des difficultés analytiques et du risque élevé de contamination des échantillons lors du processus analytique. En outre, les débris de plastique en milieu marin contiennent des additifs comme les PAEs, qui sont ajoutés lors de l’étape de fabrication du plastique. Dans la première partie de cette thèse, une méthode analytique a été optimisée et validée pour la détermination de 8 PAEs à l'état de traces en milieu marin. Brièvement, 1L d'échantillon filtré est passé à travers des cartouches de verre contenant 200 mg d'Oasis HLB, puis élué à l’aide de 6mL d'acétate d'éthyle. Notre méthode donne des rendements d’extraction compris entre 95 et 115 % et des blancs acceptables. Dans un second temps, un suivi annuel de la contamination de la Baie de Marseille a été effectué de décembre 2013 à novembre 2014. Les résultats ont montré la présence de 7 PAEs, avec des concentrations totales variant de 130 à 1330 ng L-1. Dans la dernière partie de cette thèse, deux échantillons de plastique communs (sac de poubelle et gaine de câble électrique) ont été incubés dans de l'eau de mer naturelle dans des conditions contrôlées de laboratoire, de manière à évaluer la migration de PAEs depuis ces matériaux en fonction de différentes conditions environnementales comme la température, la présence de lumière, ou encore la présence de bactéries. / Phthalic Acid Esters (PAEs) are a group of emerging organic contaminants that have become a serious issue because of their ubiquitous presence on the marine environment worldwide and for the endocrine disrupting effects in animals and humans. However, little is known about their distribution in the Ocean, mainly because of analytical difficulties and the high possibility of ambient sample contamination. Plastic debris in marine environment includes resin pellets, macro- and microplastic fragments, and contains additives such as PAEs that might be released in the aquatic environment in unknown proportion. In our work, we improved an analytical method for the determination of 8 PAEs, at trace levels in marine and fresh waters. In the first part of the thesis, the method was validated for different seawater salinities and wastewater treatment plant outlet. By passing 1 L of sample through glass cartridges packed with 200 mg of Oasis HLB and eluted with 6 mL of ethyl acetate, the recoveries of 8 PAEs ranged from 95 to 115 % with acceptable blank values (below 0.4-4.0 % of the masses measured in different seawater samples). In a second part, PAE distribution in the Marseille Bay has been evaluated though a one-year monitoring from December 2013 to November 2014. The results showed the occurrence of six PAEs with total concentrations ranging from 130 to 1330 ng L-1. In the last part of this thesis, two common plastic samples as trash plastic bags and insulation layer of electric cables were incubated in natural seawater in laboratory conditions and studied for the release of PAE. Release ws observed for the different PAEs with kinetics varying according to the plastic type.

Regulation of the inflammatory response is essential for the successful resolution of inflammation, and restoration of normal tissue homeostasis. Eosinophils are granulocytic cells of the innate immune system historically considered to be primarily involved in the defence against parasitic infection. Eosinophils are also key effector cells in the allergic inflammatory response, initiation of which is associated with the recruitment and activation of eosinophils culminating in the release of their intracellular granule contents. Eosinophil granules contain a range of cytotoxic proteins (major basic protein, eosinophil cationic protein and eosinophil peroxidase) that act to destroy infectious and parasitic organisms. However, these cytotoxic proteins can also cause damage to surrounding host tissue cells. The resolution of the inflammatory response acts to limit the extent of eosinophil-mediated tissue damage. Programmed cell death (apoptosis) of eosinophils represents an important component of this resolution process, limiting release of granule contents and triggering efferocytosis (the removal of apoptotic cells by phagocytes). Apoptosis is initiated by the activation of intracellular caspases, a family of cysteine proteases. Caspase activation primarily occurs as a result of changes in the balance of intracellular pro- and anti-apoptotic Bcl-2 family proteins. Mcl-1, an anti-apoptotic Bcl-2 protein has been shown to play a pivotal role in the regulation of neutrophil apoptosis. Pharmacological down-regulation of Mcl-1 initiates apoptosis and promotes the resolution of neutrophil-dominant inflammation. The importance of Mcl-1 in the regulation of apoptosis was shown using cyclin-dependent kinase inhibitors (CDKis), where induction of neutrophil apoptosis by CDKis was due to down-regulation of intracellular Mcl-1. Apoptotic cells display distinct surface molecules known as ‘eat-me’ signals that identify them for phagocytosis by macrophages and other phagocytes. One key receptor involved in the removal of apoptotic cells from tissue is the receptor tyrosine kinase Mer, a member of the Tyro3/Axl/Mer (TAM) family, which recognises the ‘eat me’ signal phosphatidylserine expressed on apoptotic cells. In the absence of Mer expression, clearance of apoptotic cells is compromised delaying the resolution of neutrophil-dominant inflammation. However, the roles of Mcl-1 and Mer in eosinophil apoptosis and clearance, respectively, and the resolution of allergic inflammation are not known. Asthma is a chronic inflammatory lung disease characterised by shortness of breath, airway obstruction, wheeze, non-specific bronchial hyper-responsiveness, excessive airway mucus production and an eosinophil dominant inflammatory infiltrate. The persistent presence of eosinophils in the lung, in chronic asthma, is likely due to a combination of excessive eosinophil recruitment and activation together with impaired eosinophil apoptosis. Investigation into the underlying mechanisms of these processes in allergic airway disease is of critical importance, as blocking eosinophil recruitment and/or promoting eosinophil apoptosis could provide a therapeutic approach to reduce associated eosinophil-mediated tissue damage. Understanding the regulation of eosinophil apoptosis and phagocytic clearance may identify novel pharmacological targets to enhance the resolution of allergic inflammation. We hypothesise that Mcl-1 and Mer play vital roles in the successful resolution of allergic airway inflammation. To investigate this hypothesis, we have used pharmacological and genetic manipulation of intracellular eosinophil Mcl-1 levels, and phagocyte Mer expression, to determine the role they play in the regulation of eosinophil apoptosis and phagocytic clearance of apoptotic eosinophils, respectively. Human and mouse eosinophils were cultured, and rates of constitutive and CDKi-induced apoptosis were determined, to investigate eosinophil apoptosis in vitro. Mice expressing human Mcl-1 (hMcl-1) were used to determine the effect of over-expression of Mcl-1 on eosinophil viability in vitro. The effect of hMcl-1 on eosinophil viability and disease severity in vivo was determined using an ovalbumin-induced model of allergic airway inflammation, which mimicked the symptoms of human asthma. Apoptotic eosinophils were co-incubated with macrophages in vitro to investigate the capacity for phagocytosis by different macrophage populations. Apoptotic cell clearance was further investigated using a Mer-kinase-dead mouse, which lacked Mer expression, to determine the role of Mer-dependent phagocytosis on the process of resolution of inflammation in vivo. Over-expression of Mcl-1 in eosinophils significantly delayed both constitutive and CDKi-induced apoptosis in vitro. In vivo in the ovalbumin-induced model of allergic airway inflammation, over-expression of Mcl-1 resulted in a significantly increased number of eosinophils in the lung and delayed rate of resolution of allergic airway inflammation. Alveolar and bone marrow-derived macrophages exhibited Mer-dependent phagocytosis of eosinophils, which was significantly reduced by an inhibitor of Mer kinase activity (BMS777607) or lack of macrophage Mer expression. The absence of Mer expression resulted in a significant increase in the number of apoptotic eosinophils in the lung together with a delayed rate of resolution of allergic airway inflammation in vivo. Together this work has shown that delayed rates of eosinophil apoptosis and impaired phagocytic clearance both delayed the resolution of allergic airway inflammation. These data suggest that both Mcl-1 and Mer are pivotal for the successful regulation of eosinophil apoptosis and phagocytic clearance of apoptotic eosinophils in asthma and may provide attractive novel therapeutic targets.

A la suite de nombreuses illustrations et validations au niveau fondamental, la chimie de molécules carbo-mères s'est récemment orientée vers des cibles fonctionnelles en termes de perspectives d'applications (" carbo-matériaux " moléculaires). C'est ainsi que de telles molécules expansées en carbone ont récemment montré des propriétés remarquables dans les domaines de la conductivité sur molécule unique (SMC) ou de l'absorption à deux photons (TPA). La considération de cibles de types fondamentalement nouveaux " reste cependant nécessaire en préliminaire à l'étude de propriétés nouvelles aussi. Le travail décrit dans ce manuscrit présente essentiellement les résultats concernant la synthèse de carbo-quinoïdes et de carbo-benzénoïdes, deux types de structures carbo-mères qui n'avaient jamais été envisagées expérimentalement auparavant. Le premier chapitre est un résumé bibliographique décrivant notamment la synthèse et les propriétés de molécules carbo-mères aromatiques, et plus généralement hautement pi-conjuguées (carbo-benzènes, carbo-cyclohexadiènes, carbo-oligoacétylènes...) Le second chapitre porte sur l'étude complète des trois régioisomères, " ortho ", " para ", et " meta " du tétraphényl-carbo-benzène, dont les deux premiers représentants avaient été partiellement décrits. Le troisième chapitre décrit la synthèse et l'étude du premier exemple de carbo-quinoïde, ainsi que sa transformation rédox réversible en carbo-benzènes, illustrant ainsi la " pro-aromaticité redox " des carbo-quinoïdes vis-à-vis de leurs analogues oxydés carbo-benzènes. Le quatrième et dernier chapitre est consacré à la synthèse et l'étude d'un carbo-benzénoïde, le carbo-naphtalène, pouvant être considéré comme le plus petit fragment polycyclique condensé d'alpha-graphyne, un matériau largement étudié au niveau théorique mais encore inconnu expérimentalement à ce jour. Les propriétés physico-chimiques et spectroscopiques de carbo-naphtalène sont comparées à celle du carbo-benzène monocyclique correspondant, dont la synthèse est aussi détaillée. / Following numerous illustrations and validations at the fundamental level, the chemistry of carbo-meric molecules was recently directed towards functional targets in terms of application prospects (molecular "carbo-materials'). Such carbon-expanded molecules have indeed recently been shown to exhibit remarkable properties in the areas of single molecule conductivity (SMC) or two-photon absorption efficiency (TPA). The consideration of target of fundamentally "new types" remains necessary in view of the study of new properties as well. The work described in this manuscript focus mainly on results concerning the synthesis of carbo-quinoids and carbo-benzenoids, two types of carbo-meric structures that had not been considered hitherto. The first chapter is a bibliographic summary describing the synthesis and properties of carbo-meric molecules, either aromatic or, more generally, highly pi-conjugated (carbo-benzenes, carbo-cyclohexadienes, carbo-oligoacetylenes...) The second chapter focuses on the complete study of the three regioisomers, "ortho", "para" and "meta" of tetraphenyl-carbo-benzene, the first two representatives having been partly described previously. The third chapter describes the synthesis and study of the first example of carbo-quinoid and its reversible redox transformation to carbo-benzenes, illustrating the "redox pro-aromaticity" of carbo-quinoid with respect to their oxidized carbo-benzenic analogues. The fourth and final chapter is devoted to the synthesis and study of a carbo-benzenoid, carbo-naphthalene, which can be regarded as the smallest condensed polycyclic fragment of alpha-graphyne, a material widely studied at the theoretical level but remaining unknown experimentally to date. The physicochemical and spectroscopic properties of carbo-naphthalene are compared to that of the corresponding monocyclic carbo-benzene, the synthesis of which is also detailed.

Submitted by Nathalya Silva (nathyjf033@gmail.com) on 2017-05-22T20:31:59Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_TarefasIntermediariasModelo.pdf: 2270740 bytes, checksum: 8046eff632e5c6fe2cd6f6c7f7c8d468 (MD5) / Approved for entry into archive by Edisangela Bastos (edisangela@ufpa.br) on 2017-05-31T16:30:59Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_TarefasIntermediariasModelo.pdf: 2270740 bytes, checksum: 8046eff632e5c6fe2cd6f6c7f7c8d468 (MD5) / Made available in DSpace on 2017-05-31T16:30:59Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_TarefasIntermediariasModelo.pdf: 2270740 bytes, checksum: 8046eff632e5c6fe2cd6f6c7f7c8d468 (MD5) Previous issue date: 2014-05-17 / Este trabalho trata da articulação e integração de organizações praxeológicas anunciadas pelas pesquisas a luz da teoria antropológica do didático, em particular, entre as organizações referentes as noções de frações e de operações com frações que vivem em uma dada instituição de ensino. Essa problemática é evidenciada a partir de um Modelo Epistemológico de Referência - MER aqui proposto que permite analisar e reconstruir organizações praxeológicas sobre noções e operações, de adição e subtração, de frações em que revela o papel de praxeológicas intermediárias a partir da epistemologia funcional dos objetos da matemática escolar. / This work deals with the articulation and integration of organizations praxeological announced by research the light of anthropological theory of didactic, in particular, between organizations regarding the concepts of fractions and operations with fractions that live in a given institution of education. This problematic is evident from an Epistemological Reference Model - ERM proposed here allows us to analyze and reconstruct praxeological organizations about notions and operations, addition and subtraction of fractions in revealing the role of intermediary praxeological from the functional epistemology of objects of school mathematics.

En s’inscrivant dans le champ des études transnationales, cette thèse souhaite analyser l'évolution de la politique d’attention menée par le Viêt Nam à l'égard de ses exilés (Việt Kiều) de 1945 à 2009. Il s'agit d’étudier, à travers le prisme du concept de nationalisme à distance (ou nationalisme transnational), comment ce Parti-État est entré en interaction avec son champ migratoire afin de l’associer à la réalisation de ses desseins nationaux. La première partie de cette thèse expose les raisons pour lesquelles la République démocratique du Viêt Nam (RDVN) (1945-1976) a, dès sa création, intégré les exilés vietnamiens à son processus de construction nationale pour ensuite les solidariser à son effort de guerre. Dans la seconde partie, nous verrons que la paix revenue, la désormais République socialiste du Viêt Nam (RSVN) rencontre des difficultés pour faire évoluer ses relations avec les exilés (1975-1992). Ces hésitations, freinant la concrétisation d’une politique pragmatique au service du développement économique du pays, s’expliquent essentiellement par l’anticommunisme virulent qui s'est développé dans la communauté outre-mer. La troisième partie s’attache à exposer les moyens mis en œuvre (diplomatiques, médiatiques, juridiques) par le Viêt Nam pour normaliser sa présence au sein des communautés vietnamiennes outre-mer (1992-2009). Nous verrons en conclusion qu’en deçà des ses réserves idéologiques et sécuritaires, le Parti-État vietnamien a sans cesse porté de l’intérêt aux Việt Kiều et s’est efforcé d’adapter son nationalisme à distance en fonction de ses besoins et des caractéristiques de son champ migratoire. / In the field of transnational studies, this thesis aims to analyze the evolution of Vietnam's policy towards its exiles (Việt Kiều) from 1945 to 2009. It is to study, through the concept of long -distance nationalism (or transnational nationalism), how this Party-State interacted with its migratory population in order to incorporate it into the make it part of the national goals. The first section of this thesis explains why the Democratic Republic of Viêt Nam (DRVN) (1945-1976), from its inception, integrated the Vietnamese exiles into its national construction process in order to have them join in its war effort. In the second part, we will see that with the return of peace, the country known from this moment on as the Socialist Republic of Viêt Nam (SRVN) encountered difficulties advancing its relations with the exiles (1975-1992). These setbacks, hindering the realization of a pragmatic economic development policy for the country, can be largely explained by the virulent anticommunism that developed in the overseas community. The third part aims to explain the means (diplomatic, media, and legal) used by Vietnam to normalize its presence in the Vietnamese communities overseas (1992-2009). In conclusion, we will see, despite its ideological and security reservations, that the Vietnamese Party-State has always been interested in the Việt Kiều and has sought to adapt its concept of long-distance nationalism according to its needs and the characteristics of its migratory population.

Entre le XIIIe siècle et le XVIIe siècle, se constitue un vocabulaire nautique spécifique, celui de la marine du Levant, différent de celui de la marine du Ponant utilisé en Atlantique. Ce vocabulaire est né du voyage dans le temps des mots provenant de l’indo-européen, du latin et du grec, mais sa spécificité vient des échanges, du voyage des mots dans tous l’espace méditerranéen qui permet à toutes les langues méditerranéennes de s’enrichir mutuellement. Les récits de voyage à Jérusalem constituent une source importante car ils sont rédigés par des hommes qui n’ont jamais auparavant vu la mer et qui vivent leur première expérience de navigation ; ils ont tout à apprendre pour pouvoir transmettre leur expérience à leurs lecteurs. Le métissage linguistique méditerranéen est le fait des marins qui transmettent aux marchands et aux voyageurs qui sillonnent la Méditerranée. Quand un mot domine et se répand dans d’autres langues cela signifie qu’il appartient à une langue d’une nation dominante soit dans ses techniques de navigation, soit par sa puissance maritime.Les écrivains voyageurs racontent leur navigation en montrant leurs sentiments, en exprimant leur admiration pour les spectacles nouveaux qu’ils découvrent. Comme la mer est un élément inconnu, elle engendre très souvent la peur qu’il faut surmonter, le voyage est une épreuve nécessaire et enrichissante. La constitution d’un vocabulaire spécifique montre qu’au delà des guerres, de la course, des fortunes de mer, des hommes se sont parlés, se sont entendus, ont construitensemble les outils nécessaires pour nommer les chose, c’est-à-dire les comprendre et se comprendre. / Between the XIIIth century and the XVIIth century, a specific nautical vocabulary is building, vocabulary of Levant navy of the different from Ponant one used in the Atlantic. This vocabulary come from the travel, in all the Mediterranean space, of the words in the time, from Indo-European, Latin and Greek languages. This exchanges allow all languages Mediterranean learn from each other. Travel stories in Jerusalem constitute an important source because they are drafted by men who never have seen previously sea and who live their first experience of sailing; they have to learn everything to be able to transmit their experience to their readers. The Mediterranean linguistic crossbreeding is the fact of the sailors who transmit to the traders and to the travelers who cross the Mediterranean Sea. The writers-travelers tell their navigation by showing their feelings, by expressing their admiration for the new spectacles which they discover. As sea is an unknown element, it very often generates fear. The sailing time is a necessary and rewarding event. The constitution of a specific vocabulary shows that beyond wars, corsairs, perils of sea, the men spoke to each other, built together the necessary tools to name things, it means understand its and understand each other.

La modélisation a été utilisée comme outil pour améliorer la compréhension des processus physiques et biologiques observés pendant la campagne pluridisciplinaire DYNAPROC 2 (DYNamique des PROCessus rapides dans la colonne d'eau) qui a eu lieu dans la zone centrale de la mer Ligure en septembre-octobre 2004. Cette campagne avait pour objectif l'étude des phénomènes physiques et biologiques qui agissent à courte échelle de temps lors de la transition saisonnière entre l'oligotrophie estivale et la mésotrophie automnale. L'un des éléments les plus marquants de la campagne est le passage de deux lentilles d'eau dessalée dans la zone de mesure que l'on pensait être isolée des apports latéraux. Dans ce travail, nous avons dans un premier temps appliqué un modèle 1D couplé physique-biologie aux données de la campagne. Le réseau trophique simulé comporte dix variables d'états : trois sels nutritifs, trois classes de phytoplancton, deux classes de zooplancton et deux types de détritus. Les résultats ont montré que les principales différences entre ce modèle et les mesures avaient lieu pendant les intrusions d'eau dessalée. Dans un deuxième temps, nous avons testé deux méthodes d'assimilation de données : une méthode classique de relaxation aux données de température et une méthode que nous avons développée, qui est basée sur l'assimilation des variations de profondeur des isopycnes (méthode IDA, Isopycnal Depth Adjustment). L'évaluation des performances relatives des trois modèles a été effectuée avec des diagrammes de Taylor et a montré que le modèle IDA était le plus performant dans la représentation des évènements observés. Cette étude a permis de caractériser les propriétés de la masse d'eau dessalée, de calculer les flux de matière journaliers et de définir les contributions relatives de la physique et de la biologie à l'évolution de la zone productive au large de la mer Ligure.