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The solar wind, magnetosphere and ionosphere are coupled by magnetohydrodynamic waves, and this gives rise to new and often unexpected behaviours that cannot be produced by a single, isolated part of the system. This thesis examines two broad instances of coupling: field-line resonance (FLR) which couples fast and Alfvén waves, and magnetosphere-ionosphere (MI-) coupling via Alfvén waves. The first part of this thesis investigates field-line resonance for equilibria that vary in two dimensions perpendicular to the background magnetic field. This research confirms that our intuitive understanding of FLR from 1D is a good guide to events in 2D, and places 2D FLR onto a firm mathematical basis by systematic solution of the governing equations. It also reveals the new concept of ‘imprinting’ of spatial forms: spatial variations of the resonant Alfvén wave correlate strongly with the spatial form of the fast wave that drives the resonance. MI-coupling gives rise to ionosphere-magnetosphere (IM-) waves, and we have made a detailed analysis of these waves for a 1D sheet E-region. IM-waves are characterised by two quantities: a speed v_{IM} and an angular frequency ω_{IM} , for which we have obtained analytic expressions. For an ideal magnetosphere, IM-waves are advective and move in the direction of the electric field with speed v_{IM}. The advection speed is a non-linear expression that decreases with height-integrated E-region plasma-density, hence, wavepackets steepen on their trailing edge, rapidly accessing small length-scales through wavebreaking. Inclusion of electron inertial effects in the magnetosphere introduces dispersion to IM-waves. In the strongly inertial limit (wavelength λ << λ_{e} , where λ_{e} is the electron inertial length at the base of the magnetosphere), the group velocity of linear waves goes to zero, and the waves oscillate at ω_{IM} which is an upper limit on the angular frequency of IM-waves for any wavelength. Estimates of v_{IM} show that this speed can be a significant fraction (perhaps half) of the E_{⊥} × B_{0} drift in the E-region, producing speeds of up to several hundred metres per second. The upper limit on angular frequency, ωIM , is estimated to give periods from a few hundredths of a second to several minutes. IM-waves are damped by recombination and background ionisation, giving an e-folding decay time that can vary from tens of seconds to tens of minutes. We have also investigated the dynamics and steady-states that occur when the magnetosphere-ionosphere system is driven by large-scale Alfvénic field-aligned currents. Steady-states are dominated by two approximate solutions: an ‘upper’ solution that is valid in places where the E-region is a near perfect conductor, and a ‘lower’ solution that is valid where E-region depletion makes recombination negligible. These analytic solutions are extremely useful tools and the global steady-state can be constructed by matching these solutions across suitable boundary-layers. Furthermore, the upper solution reveals that E-region density cavities form and widen (with associated broadening of the magnetospheric downward current channel) if the downward current density exceeds the maximum current density that can be supplied by background E-region ionisation. We also supply expressions for the minimum E-region plasma-density and shortest length-scale in the steady-state. IM-waves and steady-states are extremely powerful tools for interpreting MI-dynamics. When an E-region density cavity widens through coupling to an ideal, single-fluid MHD magnetosphere, it does so by forming a discontinuity that steps between the upper and lower steady-states. This discontinuity acts as part of an ideal IM-wave and moves in the direction of the electric field at a speed U = \sqrt{v_{IM} {+} v_{IM} {-}}, which is the geometric mean of v_{IM} evaluated immediately to the left and right of the discontinuity. This widening speed is typically several hundreds of metres per second. If electron inertial effects are included in the magnetosphere, then the discontinuity is smoothed, and a series of undershoots and overshoots develops behind it. These undershoots and overshoots evolve as inertial IM-waves. Initially they are weakly inertial, with a wavelength of about λ_{e}, however, strong gradients of ω_{IM} cause IM-waves to phase-mix, making their wavelength inversely proportional to time. Therefore, the waves rapidly become strongly inertial and oscillate at ω_{IM}. The inertial IM-waves drive upgoing Alfvén waves in the magnetosphere, which populate a region over the downward current channel, close to its edge. In this manner, the E-region depletion mechanism, that we have detailed, creates small-scale Alfvén waves in large-scale current systems, with properties determined by MI-coupling.

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Les techniques d’assistance médicale à la procréation particulièrement l’induction de l’ovulation, la maturation in vitro des ovocytes et la culture embryonnaire prolongée impliquent la manipulation des gamètes ainsi que les embryons à des moments critiques de leur maturation et développement qui sont également des étapes clé du remodelage épigénétique. Par conséquent, elles pourraient interférer avec la reprogrammation épigénétique, en particulier la mise en place de la méthylation des gènes soumis a empreinte au cours de l'ovogenèse, ou son maintien au cours du développement préimplantatoire. Afin d’évaluer ce risque nous avons analysé le profil de méthylation de KvDMR1, qui régule l’expression de KCNQ1OT1, dans des ovocytes humains mûris in vivo ou in vitro, provenant de patientes stimulées ou non. Nos résultats montrent que la mise en place de la méthylation au niveau de KvDMR1 se poursuit au cours de la maturation de l’ovocyte du stade VG au stade MII, in vivo et in vitro et que l’induction ovarienne des patientes génère des ovocytes épigénétiquement immatures. Par ailleurs, l’étude de la méthylation de H19 DMR qui régule l’expression d’Igf2 et H19 dans des embryons d’ICSI, atypiques bloqués en culture prolongée et dans les spermes correspondants met en évidence une hypométhylation de l'allèle paternel et une méthylation de l'allèle maternel dans certains embryons, sans que l'on puisse établir de lien entre les dérégulations de l’empreinte et l’arrêt du développement au stade blastocyste. / Assisted reproductive technologies particularly the induction of ovulation, oocytes in vitro maturation, and prolonged embryo culture require in vitro manipulation of gamete and embryos at critical times of their maturation and development. In consequence, they may interfere with epigenetic reprogramming and affect particularly demethylation and remethylation of imprinted genes. To evaluate such a risk, we have determined the methylation profile of KvDMR1, the region that regulates KCNQ1OT1 imprinted gene, in human oocytes retrieved from stimulated or unstimulated cycles, at different phases of their maturation in vivo or in vitro. Our results show that the timing of establishment of the methylation profile of KvDMR1 covers the maturation phase of oocyte growth, in vivo and in vitro, and that hyperstimulation likely recruits young follicles epigenetically immature. Analysis of the methylation profile of H19DMR (DMR of IGF2/H19) in atypical ICSI embryos and corresponding sperm suggests that imprinting disorders are not responsible of embryo developmental failure prior the blastocyst stage.

La Néoplasie Endocrinienne Multiple de type 1 (NEM1) est une maladie génétique qui associe hyperparathyroïdie primaire, tumeurs neuroendocrines digestives et adénomes hypophysaires. Elle est due à des mutations non récurrentes du gène MEN1, parfois difficile à classer. Nous avons rassemblé et analysé les données cliniques et génétiques de 1676 patients français porteurs d’une variation de MEN1 des 4 laboratoires experts du groupe TENGEN. De ce travail, nous avons alimenté une base de données de variants (UMD MEN1) et établir le profil mutationnel de MEN1 en France. Dans une seconde partie, nous avons établi des recommandations pour la classification des variants faux sens de MEN1 en adaptant les Guidelines de l’ACMG-AMP (American College of Medical Genetics).Le Syndrome de McCune-Albright (SMA) est du à des mutations postzygotiques activatrices récurrentes du gène GNAS, responsables d’un mosaïcisme somatique, souvent indétectables dans le sang. En utilisant une technique de PCR quantitative ultrasensible, le taux de détection des mutations R201C et R201H est de 50% dans le sang de 16 patients présentant 1 à 3 lésions majeures du SMA. Pour la 1ere fois, nous avons retrouvé ces mutations dans l’ADN circulant de 3/4 patients testés.Ces mutations sont retrouvées aussi dans 30 à 40% des adénomes somatotropes. Le locus GNAS est soumis à empreinte parentale, responsable d’une expression mono-allélique de GNAS dans certains tissus comme l’hypophyse. Dans une série de 57 adénomes somatotropes nous avons montré une perturbation de l’empreinte de GNAS, associée à une relâche de l’empreinte mais n’entraînait pas d’augmentation de l’expression du gène GNAS. / The Multiple Endocrine Neoplasia 1 (MEN1) is due to MEN1 mutations and characterized by a broad spectrum of lesions including hyperparathyroidism, pituitary adenomas and neuroendocrine tumors. Missense variants are frequent and could lead wrong interpretation. We collected and analyzed all the 370 variants of 1676 patients sequenced for ten years by the TENGEN network (French oncogenetics of neuroendocrine tumors). We registered them in the UMD MEN1 database. Then, consensus was reached to validate adjustments to the ACMG-AMP guidelines for MEN1 locus-specific interpretation of missense variants. The McCune-Albright syndrome (MAS) is a rare pediatric mosaic genetic disorder. MAS results from recurrent post-zygotic GNAS mutations, not detectable in blood DNA by Sanger. We develop an ultrasensitive quantitative PCR using digital droplet PCR™ (ddPCR™) in order to target the R201C and R201H GNAS mutations. After a validation study, we clinically evaluated ddPCR™ in the whole blood DNA or circulating cell-free DNA (ccfDNA) of patients presented with at least 1 MAS lesion. First we detected in ccfDNA the mosaic somatic GNAS mutant. The ddPCR™ showed a mutation detection rate of 50% in blood DNA of the 16 included patients and 3/4 in ccfDNA.GNAS mutations are also reported in 30 to 40% of somatotroph tumors. GNAS is encoded by an imprinted locus, responsible for a mono-allelic expression in pituitary. We explored the GNAS locus methylation status of 57 somatotroph adenomas and showed disturbance. We studied the impact on GNAS, SST2R and AIP expression of this disturbance. We showed an imprinting relaxation not associated with an increased expression of GNAS.

GNAS est un locus complexe soumis à l'empreinte parentale. Il code pour cinq transcrits alternatifs dont l’expression est régulée de manière parentale, tissulaire et développementale : la sous-Unité alpha stimulatrice de la protéine G hétérotrimérique (Gαs), XLαs, NESP55, et deux ARNnc, A/B et GNAS-AS1. Gαs est une protéine clé dans la transduction hormonale partageant avec XLαs la capacité de produire l'AMPc intracellulaire après stimulation des récepteurs couplés à Gαs.Dans la première partie de ma thèse, je me suis concentrée sur l'étude du rôle des transcrits de GNAS, en particulier XLαs, dans la croissance fœtale et post-Natale. J’ai profité du modèle unique des pseudohypoparathyroïdies (PHPs), pathologies humaines rare de l’empreinte, causées par des anomalies génétiques ou épigénétiques du locus GNAS altérant le dosage génique des transcrits de GNAS. La croissance anormale est une caractéristique majeure des PHPs.Dans la deuxième partie de ma thèse, j’ai étudié le profil épigénétique du locus GNAS (méthylation de l'ADN et expression des transcrits) dans les cellules souches humaines embryonnaires -HESCs-, dans les cellules pluripotentes induites dérivées à partir de fibroblastes de sujets sains -IPSCs- et dans les cellules redifférenciées en cellules souches neurales et mésenchymateuses. La caractérisation précise du locus humain GNAS en physiologie (cellules souches) et pathologie (PHP) est essentielle pour une meilleure compréhension des processus développementaux importants comme la croissance. L'exploration du phénotype "croissance" de différents types de PHPs a permis de mieux comprendre le rôle des transcrits du locus GNAS dans la physiologie et la physiopathologie. L'analyse de cellules des PHPs a permis de mieux caractériser l’impact des anomalies moléculaires du locus GNAS en pathologie humaine. Les hiPSCs peuvent être un outil utile pour étudier les modifications épigénétiques au niveau du locus GNAS. / GNAS is a complex locus subjected to parental imprinting encoding five parental-, tissue- and developmental-Manner regulated transcripts : the alpha stimulatory subunit of the G protein (Gαs), XLαs, NESP55, and two ncRNAs, A/B and the antisens GNAS-AS1. Gαs is a key protein in hormonal signaling sharing with XLαs the ability to produce intracellular cAMP upon stimulation of Gαs-Coupled receptors. In the first part of my thesis, I focused on studying the role of the GNAS transcripts, particularly XLαs, in fetal and postnatal growth. I took advantage of the unique model of pseudohypoparathyroidism (PHP), a rare human disease, caused by genetic or epigenetic abnormalities at the GNAS locus leading to various combinations of GNAS transcripts alterations. Abnormal growth appears to be a major feature of PHP. In the second part of my thesis, I studied the epigenetic pattern of GNAS (DNA methylation and transcripts expression) in human embryonic stem cells -HESCs-, in induced pluripotent stem cells -IPSCs- derived from fibroblasts from healthy individuals, and in cells re-Differentiated from these stem cells in neuronal and mesenchymal cells. The precise characterization of the human GNAS locus in physiology (stem cells) and pathology (PHP) is critical for a better understanding of major processes like growth. Through exploration of the "growth" phenotype of different groups of PHPs we have participated to the better understanding of the role of the GNAS transcripts in the physiology and pathophysiology. Human iPSCs may be an useful tool to study epigenetic modifications at the GNAS locus.

Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood.

Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood.

Abstract Integrated optical (IO) sensor allowing sensitive, label-free, real-time and multi-parameter monitoring of bio-molecular interactions are conventionally fabricated with inorganic dielectrics inherited from CMOS manufacturing technology. Polymers as complement materials to inorganic dielectrics are becoming to have an increasing market share for IO circuits in optical communications networks owing to its good optical properties, versatile processibility and low cost. This work aims at developing disposable low-cost biosensors based mainly on polymeric materials, with a performance comparable to inorganic-dielectric based IO biosensors. This thesis describes the development of polymer IO biosensors based on the Young interferometer (YI) transducer platform for ambient noise compensation and a complete periodic intensity fringe pattern. Three different waveguide configurations were utilized, taking into consideration operational simplicity, fabrication simplicity and enhanced sensitivity. Among the developed polymer biosensors, an unconventional interferometer structure: a vertically placed dual-slab waveguide interferometer and an inverted rib waveguide configuration were employed. To enhance the sensitivity of the waveguides, deposition of Ta2O5 high index coating was performed on the rib waveguide configuration. Along with the development of polymer biosensors based on the inverted-rib waveguide configuration, a fabrication process was also developed featuring UV-imprinting and spin coating. The simple two-step fabrication process demonstrated using a polymer mold is potentially transferable to the roll-to-roll manufacture process. Calibration of the developed sensors was performed by homogeneous refractive index (RI) sensing with glucose de-ionized water solutions. By investigating an antibody – antigen binding interaction involving C-reactive protein and its conjugates, this thesis confirmed the applicability of the developed sensors to specific molecule detection. Moreover, to establish the influence of water molecular absorption on measurement stability, an evaluation was carried out on the polymeric waveguide. Finally, the thesis presented a comparison between the developed sensors, exploring their sensitivities, stabilities, limits of detection (LODs) and other aspects related to operation and fabrication. The results indicated that the Ta2O5-coated polymer waveguide sensor had a high sensing capability. In homogeneous RI sensing, the achieved detection limits were 9×10-7 RIU (refractive index unit), i.e., three times the noise level, and 270 fg/mm2 for surface mass density. / Tiivistelmä Integroidulla optiikalla toteutetut anturit mahdollistavat biomolekulaarisen vuorovaikutuksen tutkimisen käyttäen herkkiä moniparametrisia ja merkkiaineettomia menetelmiä. Näiden bioantureiden valmistukseen käytetään tavallisesti CMOS-teknologian piiristä tuttuja epäorgaanisia puolijohteita ja eristemateriaaleja. Viime aikoina on kuitenkin polymeeristen materiaalien käyttöä integroidussa optiikassa tutkittu merkittävästi johtuen polymeerien hyvistä optisista ominaisuuksista, monipuolisesta työstettävyydestä ja edullisista kustannuksista. Tämän työn tarkoituksena on kehittää edullisia, kertakäyttöisiä, pääasiallisesti polymeerisistä materiaaleista valmistettuja bioantureita, jotka vastaavat suorituskyvyltään epäorgaanisista materiaaleista valmistettuja integroidun optiikan antureita. Tässä työssä kehitetyt polymeeriset integroidun optiikan bioanturit perustuvat Youngin interferometriin mahdollistaen ympäristökohinan kompensoinnin ja ne tuottavat pintavuorovaikutusten tutkimiseen jaksoittaisen interferenssikuvion. Työssä hyödynnettiin kolmea erilaista valokanavarakennetta huomioiden niiden käytön helppous, valmistuksen yksinkertaisuus ja mittausherkkyys. Yksi kehitetyistä polymeerisistä bioantureista koostui päällekkäisistä kerrostetuista polymeerikerroksista. Toisen tutkitun rakenteen toiminta puolestaan perustui käänteiseen harjannevalokanavaan. Mittausherkkyyttä parannettiin pinnoittamalla polymeerirakenne Ta2O5-pinnoitteella. Näin muodostui kerrostettu komposiittivalokanava, joka oli tässä työssä tutkittu kolmas sensorirakenne. Itse bioanturien lisäksi kehitettiin myös valmistusprosessi, jossa hyödynnettiin UV-painatusta ja nestefaasipinnoitusta. Tässä työssä havaittiin lisäksi, että kehitetty yksinkertainen valmistusmenetelmä on paitsi toimiva, myös mahdollisesti siirrettävissä rullalta rullalle valmistus- ja tuotantoteknologiaan. Kehitettyjen anturien kalibrointi suoritettiin homogeenisella taitekerroinmittauksella käyttäen liuoksia, jotka valmistettiin glukoosista ja deionisoidusta vedestä. Kehitettyjen anturien soveltuvuus spesifien molekyylien tunnistamista varten todennettiin tutkimalla vasta-aineiden ja antigeenien sitoutumisreaktioita ja vuorovaikutusta C-reaktiivisella proteiinilla ja sen konjugaateilla. Lisäksi työssä tutkittiin veden absorption vaikutusta mittauksen stabiilisuuteen. Tutkimuksessa suoritettiin vertailu kehitettyjen anturien ja niiden ominaisuuksien välillä kiinnittäen huomiota mittausherkkyyteen, stabiilisuuteen, määritys- ja toteamisrajoihin ja muihin anturien valmistukseen sekä käyttöön liittyviin keskeisiin piirteisiin. Tulokset osoittavat, että Ta2O5-pinnoitetun polymeerivalokanavan mittausherkkyys oli suurin vertailluista rakenteista. Homogeenisessä taitekerroinmittauksessa saavutettu määritys- ja toteamisraja oli 9×10-7 taitekerroinyksikköä (RIU). Pintamassatiheysmittauksessa saavuttu tulos oli 270 fg/mm2.