L’objectif de cette thèse était de développer et d’optimiser de nouvelles méthodologies et approches analytiques afin d’améliorer le potentiel de l’analyse protéomique pour les études biologiques.La première partie de ce travail est consacrée à la détermination massive et exacte de la position N-Terminale des protéines (N-Terminome). Pour cela, nous avons utilisé et développé une approche basée sur une dérivation N-Terminale au TMPP. Cette méthodologie de marquage de la position N-Terminale a permis d’aborder l’étude des clivages protéolytiques des protéines exportées par le parasite P. falciparum (pathogène de la malaria) dans le globule rouge.Afin de permettre une exploitation automatique à haut débit des données de MS/MS, nous avons élaboré une nouvelle méthodologie (dénommée dN-TOP). Celle-Ci repose sur l’utilisation de TMPP portant des isotopes stables et permet ainsi d’accéder à la détermination des positions N-Terminales pour des études de N-Terminome à large échelle.La seconde partie est dédiée aux développements de différentes stratégies analytiques de quantification, aussi bien au niveau peptidique qu’au niveau protéique, appliquées à une série de problématiques biologiques. Ces optimisations ont été réalisées dans le contexte de l’étude des complexes protéiques, du dosage de prion par SRM, de quantification des glycations d’anticorps monoclonaux thérapeutiques et de l’hémoglobine HbA2 pour la standardisation des méthodes de référence. / The objective of this Ph.D. thesis was to develop and optimize new methodologies and analytical approaches to improve the potential of the mass spectrometry based proteomics.The first part of this work focused on the development of the N-Termini proteomics. This topic was addressed with a specific N-Termini chemical derivatization based on TMPP. We have shown that our method allowed both specific N-Terminomics and classical proteomics studies in the same experiment.This N-Terminus methodology was applied to study the proteolytic cleavages of the exported proteins in P. falciparum, a parasite responsible for the malaria.In order to automatize the complex and tedious informatics processsing of the MS/SM data of ourTMPP based N-Terminomics method, we have introduced a new approach (named dN-TOP), based on the use of a stable isotope labeled TMPP which made now N-Terminome proteomics compatible with high throughput studies.The second part addresses quantitative aspects of proteomics. It describes the optimization of quantitative methods at the peptide level or at the protein level for five different proteomic studies in the context of protein complex subunits, targeted SRM based prion, quantification of monoclonal antibodies glycation and hemoglobin HbA2 for reference measurement methods standardization.

Proline-rich antimicrobial peptides (PrAMPs) are promising candidates for the treatment of infections caused by highpriority human pathogens. Their mode of action consists of (I) passive diffusion across the outer membrane, (II) active transport through the inner membrane, and (III) inhibition of protein biosynthesis by blocking the exit tunnel of the 70S ribosome. We tested whether in vitro data on ribosomal binding and bacterial uptake could predict the antibacterial activity of PrAMPs against Gram-negative and Gram-positive bacteria. Ribosomal binding and bacterial uptake rates were measured for 47 derivatives of PrAMP Onc112 and compared to the minimal inhibitory concentrations (MIC) of each peptide. Ribosomal binding was evaluated for ribosome extracts from four Gram-negative bacteria. Bacterial uptake was assessed by quantifying each peptide in the supernatants of bacterial cultures. Oncocin analogues with a higher net positive charge appeared to be more active, although their ribosome binding and uptake rates were not necessarily better than for Onc112. The data suggest a complex mode of action influenced by further factors improving or reducing the antibacterial activity, including diffusion through membranes, transport mechanism, secondary targets, off-target binding, intracellular distribution, and membrane effects. Relying only on in vitro binding and uptake data may not be sufficient for the rational development of more active analogues.

Neurological disorders, including spinal cord injury, peripheral nerve injury, traumatic brain injury, and neurodegenerative diseases, pose significant challenges in terms of diagnosis, treatment, and understanding the underlying pathophysiological processes. Label-free multiphoton microscopy techniques, such as coherent Raman scattering, two-photon excited autofluorescence, and second and third harmonic generation microscopy, have emerged as powerful tools for visualizing nervous tissue with high resolution and without the need for exogenous labels. Coherent Raman scattering processes as well as third harmonic generation enable label-free visualization of myelin sheaths, while their combination with two-photon excited autofluorescence and second harmonic generation allows for a more comprehensive tissue visualization. They have shown promise in assessing the efficacy of therapeutic interventions and may have future applications in clinical diagnostics. In addition to multiphoton microscopy, vibrational spectroscopy methods such as infrared and Raman spectroscopy offer insights into the molecular signatures of injured nervous tissues and hold potential as diagnostic markers. This review summarizes the application of these label-free optical techniques in preclinical models and illustrates their potential in the diagnosis and treatment of neurological disorders with a special focus on injury, degeneration, and regeneration. Furthermore, it addresses current advancements and challenges for bridging the gap between research findings and their practical applications in a clinical setting.

Die markierungsfreie Detektion von molekularen Wechselwirkungen mittels Feldeffekt-basierter Sensoren ist eine vielversprechende Strategie zur Entwicklung einer neuen Generati-on von Biochips mit direkter elektrischer Auslesung und somit geeignet für schnelle, einfache und kostengünstige Analysen. In dieser Arbeit wurde als Transducer eine kapazitive Elektrolyt-Isolator-Silizium- (EIS) Struktur zur markierungsfreien elektrischen Detektion geladener Makromoleküle anhand ihrer intrinsischen Ladung verwendet. Als Modellsystem für die Untersuchung der im EIS-Sensor durch die Ausbildung „planarer“ bzw. „brush“-ähnlicher Molekülschichten induzierten Effekte wurden Polyelektrolyt-Multischichten (PEM) bzw. DNA-Moleküle verwendet. Die Adsorption der positiv und negativ geladenen Polyelektrolyt-Schichten an die Sensor-Oberfläche, sowie der Einfluss der Polyelektrolyt-Konzentration, der Ionenstärke und der Art des Elektrolyten auf das EIS-Signal wurden elektrochemisch untersucht. Zusätzlich wurde die Ausbildung der PEM physikalisch unter Verwendung eines Rasterkraftmikroskopes und der Ellipsometrie charakterisiert. Basierend auf Silizium-Isolator-Silizium-Strukturen wurde zum ersten Mal ein Mikroarray mit „Nanoplate“ EIS-Sensoren entwickelt, die alle auf einem einzigen Chip integriert waren. Dies ermöglicht mittels differenzieller Messanordnungen eine verlässliche Detektion der DNA-Hybridisierung bzw. -Denaturierung. Die Eigenschaften des Biosensors wurden durch Verwendung von Gold-Nanopartikeln für die Immobilisierung der DNA auf der Sensorober-fläche sowie durch eine niedrige Salzkonzentration im Messpuffer entscheidend verbessert. Die Ergebnisse dieser neuen Vorgehensweise wurden mittels Fluoreszenz-Mikroskopie vali-diert. Darüber hinaus wurde ein elektrostatisches Modell für einen EIS-Sensor mit einer „planaren“ und einen weiteren, mit „brush“-ähnlicher Molekularschicht entwickelt. Das Modell prognos-tiziert eine starke Abhängigkeit der Sensorsignalstärke von der Elektrolytkonzentration, der Ladungsdichte auf der Oberfläche und dem Abstand zwischen geladener Schicht und Sensor-oberfläche. Die Prognosen stimmten durchweg gut mit den experimentellen Ergebnissen überein. / Label-free detection of molecular interactions utilizing field-effect devices is one of the most attractive approaches for a new generation of biochips with direct electrical readout for a fast, simple and cost-effective analysis. In this study, a capacitive electrolyte-insulator-semiconductor (EIS) structure was used as transducer for the label-free electrical detection of charged macromolecules via their intrinsic charge. Polyelectrolyte multilayers (PEM) and DNA molecules were utilized as model systems to study the charge effects induced in EIS sensors by the formation of “planar”- and “brush”-like molecular layers, respectively. The layer-by-layer adsorption of positively and negatively charged polyelectrolyte (PE) layers onto the sensor surface as well as the influence of PE concentration, ionic strength and type of the applied electrolyte on the EIS sensor signal was electrochemically studied. In addition, the PEMs build-up was physically characterized using atomic force microscopy, scanning electron microscopy and ellipsometry. An array of on-chip integrated nanoplate EIS sensors based on a silicon-on-insulator structure was developed for the first time, enabling the reliable detection of DNA hybridiza-tion/denaturation in a differential measurement setup. Enhanced DNA biosensor characteris-tics were achieved by the immobilization of DNA molecules on the sensor surface via Au-nanoparticles and used low-concentrated buffer solution for the measurements. The results of this novel approach were validated by means of the fluorescence microscopy method. Furthermore, an electrostatic model for an EIS sensor modified with “planar”- and “brush”-like molecular layers was developed. The model predicts a strong dependence of the sensor signal on the electrolyte concentration, surface charge density and the distance between the charged layer and the sensor surface. This is consistently agreeing with the experimental re-sults.

Single Cell Proteomics (SCP) is an emerging discipline that contributes to a deeper understanding of individual cells' essential components. In biological systems, individual cells exhibit remarkable diversity, showcasing distinct proteomic profiles and functions. Mass Spectrometry (MS)-based techniques have become essential tools for exploring the proteomes of single cells with remarkable precision. While traditional bulk proteomics methods have been invaluable in revealing the overall protein composition of biological samples, they fall short in capturing the subtle nuances and heterogeneity among individual cells in a population. This limitation emphasizes the need for more targeted and detailed analyses to uncover the protein makeup of single cells. The MS-Based Single-Cell Proteomics technology serves as a valuable solution, providing comprehensive insight at the cellular level by analyzing proteins for identity, abundance, post-translational modifications, and interactions. This dissertation focuses on advancing single-cell proteomics through method development to enhance sensitivity and throughput. It presents a detailed protocol for a label-free single-cell proteomics workflow that integrates the cost-effective HP D100 Single Cell Dispenser and a one-hour, one-step sample preparation method. In contrast to the standard data-dependent acquisition method, the novel wide window acquisition (WWA) intentionally co-isolates and co-fragments adjacent precursors along with the selected precursor, using large isolation windows. Optimized WWA significantly increased the number of MS2-identified proteins by ≈40% compared to standard data-dependent acquisition. In a 40-minute LC gradient at ≈15 nL/min, an average of 3000 proteins per single HeLa cell was identified. Employing this platform, we compared protein expression in individual HeLa cells where the crucial autophagy gene, atg9a, was knocked out, and contrasted it with their isogenic wild-type parental line. To enhance throughput and robustness while preserving superior sensitivity at ultra-low flow rates, we developed an improved multi-column nanoLC system. This system features accelerated offline gradient generation, multiple storage sample loops with selective elution profiles, and allows for analysis as fast as every 20 minutes at 40 nL/min with close to 100% MS utilization time. Moreover, it enables continuous operation for up to 6 months without the need for column replacement. When applied to single-cell Multiple Myeloma treated with lenalidomide, this workflow identified an average of around 1300 unique protein groups.

Droplet microfluidics is an emerging technology for analysis of single cells and biomolecules at high throughput. The controlled encapsulation of particles along with the surrounding microenvironment in discrete droplets, which acts as miniaturized reaction vessels, allows millions of particles to be screened in parallel. By utilizing the unit operations developed to generate, manipulate and analyze droplets, this technology platform has been used to miniaturize a wide range of complex biological assays including, but not limited to, directed evolution, rare cell detection, single cell transcriptomics, rare mutation detection and drug screening. The aim of this thesis is to develop droplet microfluidics based methods for analysis of single cells and nucleic acids. In Paper I, a method for time-series analysis of mammalian cells, using automated fluorescence microscopy and image analysis technique is presented. The cell-containing droplets were trapped on-chip and imaged continuously to assess the viability of hundreds of isolated individual cells over time. This method can be used for studying the dynamic behavior of cells. In Paper II, the influence of droplet size on cell division and viability of mammalian cell factories during cultivation in droplets is presented. The ability to achieve continuous cell division in droplets will enable development of mammalian cell factory screening assays in droplets. In Paper III, a workflow for detecting the outcome of droplet PCR assay using fluorescently color-coded beads is presented. This workflow was used to detect the presence of DNA biomarkers associated with poultry pathogens in a sample. The use of color-coded detection beads will help to improve the scalability of the detection panel, to detect multiple targets in a sample. In Paper IV, a novel unit operation for label-free enrichment of particles in droplets using acoustophoresis is presented. This technique will be useful for developing droplet-based assays that require label-free enrichment of cells/particles and removal of droplet content. In general, droplet microfluidics has proven to be a versatile tool for biological analysis. In the years to come, droplet microfluidics could potentially be used to improve clinical diagnostics and bio-based production processes. / <p>QC 20160926</p>

Ces travaux de thèse, consacrés à l'étude et analyse quantitative d'images de phase obtenues par interférométrie à décalage quadri-latéral, ont pour but la caractérisation d'un point de vue métrologique d'un outil de mesure et de ses différentes applications. Cette technique d'interférométrie, développée initialement par la société Phasics pour les marchés de la métrologie optique et de la caractérisation de faisceaux laser essentiellement, peut aussi permettre d'obtenir la cartographie d'un champ électromagnétique complexe grâce à une mesure de front d'onde. En l'utilisant sur un microscope en condition d'imagerie, ont été obtenues des images de l'intensité et de la différence de chemin optique introduite par un échantillon semi-transparent, définissant ainsi une nouvelle technique de contraste de phase quantitatif. La première partie de cette thèse sera consacrée aux techniques en microscopie qui permettent une quantification. Nous verrons les enjeux de l'obtention de ce caractère quantitatif et ce qu'il signifie dans le cadre de différentes techniques utilisant la fluorescence. On étudiera la mesure dans le cadre d'une approximation dite "projective" réalisant certaines hypothèses. On verra quelles sont les grandeurs accessibles grâce à une mesure dans le cadre de cette approximation et quelles applications en biologie peuvent être développées concernant les éléments isotropes dans une première partie et les éléments anisotropes dans une seconde partie.Nous démontrerons la possible transposition de ces applications réalisées en deux dimensions en trois dimensions avec une résolution axiale suffisante permettant une reconstruction tomographique. / The aim of this thesis, dedicated to the study and quantitative analysis of phase images obtained thanks to quadri-wave lateral shearing interferometry, is to caracterize a metrological tool and its three proposed different applications.This work has been done in collaboration between Institut Fresnel (Marseille, France) and Phasics company (Palaiseau, France) and continues that of Pierre Bon who has been in charge the application this technique to microscopy. This interferometric technique, developped by Phasics, for optical metrology and lasers characterization, allows to record complex eletromagnetic field maps thanks to a wave front measurement. By using it in the microscope image plane, one can obtain inetnsity and optical path difference images of a semi-transparent biological sample. this technique is now considered as a new quantitative phase contrast technique.The first part of this manuscript will be a state of the art of quantitative microscopy techniques. The issues of quantification and its meanings in the framework of different fluorescent and phase based techniques will be discussed.A description of the technique that is used and its comparison with similar phase techniques will be done.The measurement, under the projective approximation, is studied leading to different variables. We show different applications concerning isotropic elements in a first part and anisotropic elements in the second one.We show how this measurement is trnasposed to the third dimensions allowing three dimensional imaging and complete reconstruction of refractive index maps of biological samples.

Des substrats SERS, élaborés selon une approche simple et à moindre coût, ont été étudiéspour la détection sans marqueurs d’ADN en vue d’applications dans le domaine du diagnostic médical.Un protocole de réduction photocatalytique assistée chimiquement conduisant à des hétérostructuresAg°/TiO2 a été optimisé. Nohttp://star.theses.fr/editeur.jsp?tefId=58411&action=save#droitsus avons montré en quoi l’utilisation d’un agent encapsulant et d’uneprocédure de nucléation-croissance permettent de contrôler la formation et l’agrégation de NPs Ag° à lasurface de couches minces TiO2. L’agrégation contrôlée des NPs conduit à des points chauds induisantune très forte amplification de l’effet SERS. Les performances des substrats SERS ont tout d’abord étévalidées par détection Raman de la molécule modèle R6G. Des études de fond, portant sur la détectionde polybases dérivées des quatre nucléobases constituant la structure de l’ADN, adénine, cytosine,guanine et thymine, ont ensuite été réalisées. Le potentiel de détection des hétérostructures Ag°/TiO2 apermis l’indexation quasi-intégrale des bandes Raman des quatre polybases étudiées, modifiées ou nonavec des groupements NH2, et nous a permis de discuter des effets d’accrochage, d’orientation etd’agencement des molécules d’ADN sur les substrats SERS. Des études complémentaires ont finalementconfirmé le potentiel de nos hétérostructures en fournissant différents aperçus sur l’hybridation despolybases et l’association de différentes polybases sur un même substrat SERS. / SERS substrates, elaborated through a simple and low-cost procedure, have been studied forthe label-free detection of DNA in the view of applications in the medical diagnostic field. A chemicallyassisted photocatalytic reduction protocol leading to an Ag°/TiO2 heterostructure has been optimized.We have shown how the use of an encapsulating agent and a nucleation-growth procedure enable tocontrol the formation and aggregation of Ag° NPs at the surface of TiO2 thin films. The controlledaggregation of NPs leads to hot points inducing a very strong amplification of the SERS effect.Performances of the SERS substrate have first been evaluated through the Raman detection of the R6Gmodel molecule. Thorough studies dealing with the detection of polybases derived from the fournucleobases constituting the DNA structure, adenine, cytosine, guanine, and thymine, have then beenconducted. The detection potential of the Ag°/TiO2 heterostructure enabled a nearly exhaustiveindexation of the Raman bands for the four studied polybases, modified or not with NH2 groups, and todiscuss on binding, orientation, and ordering effects of the DNA molecules on the SERS substrate.Complementary studies finally enabled us to confirm the potential of our heterostructure by providingdifferent insights on the polybase hybridization and the association of different polybases on a sameSERS substrate.

The electromagnetic absorption properties of plasmonic nanostructures were utilized to develop mesoscopic sites for highly efficient photothermal generation steam, SERS biosensing, and light-triggered cellular delivery uptake. Plasmonic nanostructures embedded in common thermal solutions produces vapor without the requirement of heating the fluid volume. When particles are dispersed in water at ambient temperature, energy is directed primarily to vaporization of water into steam, with a much smaller fraction resulting in heating of the fluid. Solar illuminated aqueous nanoparticle solution can drive water-ethanol distillation, yielding fractions significantly richer in ethanol content than simple thermal distillation and also produced saturated steam destroying Geobacillus stearothermophilus bacteria in a compact solar powered autoclave. Subwavelength biosensing sites were developed using the plasmonic properties of gold nanoshells to investigate the properties of aptamer (DNA) target complexes. Nanoshells are tunable core-shell nanoparticles whose resonant absorption and scattering properties are dependent on core/shell thickness ratio. Nanoshells were used to develop a label free detection method using SERS to monitor conformational change induced by aptamer target binding. The conformational changes to the aptamers induced by target binding were probed by monitoring the aptamer SERS spectra reproducibility. Furthermore, nanoshells can serve as a nonviral light-controlled delivery vector for the precise temporal and spatial control of molecular delivery in vitro. The drug delivery concept using plasmonic vectors was shown using a monolayer of ds-DNA attached to the nanoshell surface and the small molecular “parcel” intercalated inside ds-DNA loops. DAPI, a fluorescent dye, was used as the molecular parcel to visualize the release process in living cells. Upon laser illumination at the absorption resonance the nanoshell converts photon energy into heat producing a local temperature gradient that induces DNA dehybridization, releasing the intercalated molecules.

L‐glutamate is associated with several neurological disorders; thus, monitoring fast dynamics of L‐glutamate is of great importance in the field of neuroscience. Electrode miniaturization demanded by many applications leads to reduced surface area and decreased amounts of immobilized enzymes on coated electrodes. As a result, lower signal‐to‐noise ratios are observed for oxidase‐enzyme based sensors. To increase the signal‐to‐noise ratio we have developed a process to fabricate micro‐ and nano‐ structures on the microelectrode surface. Localized surface‐plasmon resonances (SPR) has been extensively used to design label‐free biosensors that can monitor receptor‐ligand interactions. A major challenge with localized SPR sensors is that they remain highly susceptible to interference because they respond to both solution refractive index changes and surface binding of the target analyte. The key concept introduced in the present work is the exploitation of transverse and longitudinal resonance modes of nanorod arrays to differentiate between bulk refractive index changes and surface interactions. The transverse bulk sensitivity of the localized SPR sensor (107 nm/RIU) remains competitive with typical single mode gold nanosphere SPR sensors. The figure of merit for the device’s cross‐sensitivity (1.99) is comparable to that of typical wavelength‐interrogated propagating SPR sensors with self referencing.