Dissertations / Theses on the topic 'Analyses en cellules uniques'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Analyses en cellules uniques.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
Laplatine, Loïc. "Résolution spatiale en microscopie par résonance de plasmon de surface à couplage par prisme." Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENY044/document.
Prism-based surface plasmon resonance (SPR) microscopy is an optical imaging technique invented in the late 60s'. Its main advantage lies in its high sensitivity to optical index or thickness variations at a metal surface. Therefore, the monitoring of biological reactions can be performed in real-time without labeling agent such as fluorescence or enzymes. Over the last 30 years, SPR microscopy has become the major technique in label-free biodetection. The field of application range from the determination of affinity constant in biochemistry to the detection of pathogenic bacteria via cellular biology. Until now, the propagation length of the surface plasmons has been considered as the spatial resolution limit. However, many examples do not support this statement. In this PhD thesis, we demonstrate that the resolution is also limited by optical aberrations induced by the prism used to couple light and surface plasmons. Thus, we are able to explain why the experimental resolution was usually worse than the predicted one. The analysis of the image formation and the quantification of aberrations lead us to suggest two new optical configurations optimized for resolution. We also analyze which metal exhibits the better trade-off between propagation length and sensitivity. Experimentally, we obtain a resolution between 1.5 and 4 μm depending on the direction, on field-of-view up to several mm2, and with a standard sensitivity for biodetection (monolayer of DNA). We are then able to observe simultaneously several thousands of individual eukaryote and prokaryote cells. Finally, we develop a prototype dedicated to the real-time monitoring of protein secretion by immune cells. The limits of SPR microscopy and the solutions which could allow this kind of study are discussed. Preliminary results on the improvement of bacterial detection are also presented
Deprez, Marie. "Étude de l’hétérogénéité cellulaire et des dynamiques de régénération de l’épithélium respiratoire sain par analyses des signatures transcriptionnelles sur cellules uniques." Electronic Thesis or Diss., Université Côte d'Azur (ComUE), 2019. http://www.theses.fr/2019AZUR6022.
Improvements made in nucleic acid sequencing and cell handling technologies now offer the opportunity to analyze simultaneously the content of numerous single cells (RNA, DNA, ...) by global and unbiased approaches. This single-cell ‘omics’ revolution provides a new framework to revisit the “Cell Theory”, elaborated over several centuries, and essentially based on morphological and functional features. The many cell modalities now accessible at single- cell level, such as their transcriptome, spatial localization, developmental trajectories, enrich considerably this definition, and set a renewed context to precisely reassess the definition of ‘cell types’, ‘cell states’ as well as their different interactions and fates.My thesis work initially set up ad hoc approaches and statistical framework to analyze appropriately these single-cell data, which deeply differ from standard bulk RNA-seq. High variance, presence of a huge percentage of null values, large volume of data are among the specific characteristics of these datasets. My work was centered on the main experimental model of my host laboratory, e.g. the human airway epithelium. Human airways are lined by a pseudostratified epithelium mainly composed of basal, secretory, goblet and multiciliated cells. Airways also constitute a true cellular ecosystem, in which the epithelial layer interacts closely with immune and mesenchymal cells. This coordination between cells ensures proper defense of the respiratory system and its correct regeneration in case of external aggression and injuries. A better understanding of the operating sequences in normal and physiopathological situations is relevant in pathologies such as chronic obstructive pulmonary disease, asthma or cystic fibrosis.First, I characterized at a single cell level the precise and cell-specific sequence of events leading to functional regeneration of the epithelium, using a 3D model of human cells. I then built a single-cell atlas of the different cell types that are lining healthy human airways from the nose to the 12th generation of bronchi.By applying computational and statistical approaches, I have identified cell lineage hierarchies and was able to reconstruct a comprehensive cell trajectory roadmap in human airways. I not only confirmed previously described cell lineages, but I have also discovered a novel trajectory that links goblet cells to multiciliated cells, identifying novel cell populations and molecular interactors involved in the process of healthy human airway epithelium regeneration. The profiling of 12 healthy volunteers then generated a dataset of 77,969 cells, derived from 35 distinct locations. The resulting atlas is composed of more than 26 epithelial, immune and stromal cell types demonstrating the cellular heterogeneity present in the airways. Its analysis has revealed a strong proximo-distal gradient of expression in suprabasal, secretory, or multiciliated cells between the nose and lung airways. My work has also improved the characterization of rare cells, including “hillock” cells that have been previously described in mice.In conclusion, this work probably represents one of the first single-cell investigations in human airways. It brings original contributions to our understanding of differentiation’s dynamics and cellular heterogeneity in healthy human airways. The resulting resource will be extremely useful for any future single-cell investigators and also for establishing a very useful joint between clinical and biological works. As such, it will constitute a reference in any future project aiming to precisely analyze specific disease conditions
Pagliaro, Sarah Beatriz De Oliveira. "Transcriptional control induced by bcr-abl and its role in leukemic stem cell heterogeneity. Single-Cell Transcriptome in Chronic Myeloid Leukemia: Pseudotime Analysis Reveals Evidence of Embryonic and Transitional Stem Cell States Single Cell Transcriptome in Chronic Myeloid Leukemia (CML): Pseudotime Analysis Reveals a Rare Population with Embryonic Stem Cell Features and Druggable Intricated Transitional Stem Cell States A novel neuronal organoid model mimicking glioblastoma (GBM) features from induced pluripotent stem cells (iPSC) Experimental and integrative analyses identify an ETS1 network downstream of BCR-ABL in chronic myeloid leukemia (CML)." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASQ032.
Chronic myeloid leukemia is a clonal hematopoietic malignancy, characterized by the acquisition of the t (9;22) translocation leading to Ph1 chromosome and its counterpart BCR-ABL oncogene, in a very primitive hematopoietic stem cell. CML is a model of targeted therapies as the proof of concept of the feasibility of targeting the tyrosine kinase (TK) activity BCR-ABL using TK inhibitors (TKI) has been shown to lead to major responses and remissions. However, the current problems encountered in these therapies are primitive leukemic stem cells resistance and their persistence which is thought to be related to the heterogeneity of the stem cells at diagnosis leading to clonal selection of cells resisting to TKI therapies. I have applied the technology of single cell transcriptome analysis to CML cells using a panel of genes involved in different pathways combined with trajectory inference analysis to the gene expression pattern. The results showed a transitional stem cell states including embryonic genes identified in CML cells at diagnosis which could contribute to LSC resistance and persistence. Furthermore, the oncoprotein Bcr-Abl is the constitutively active tyrosine kinase produced by the chimeric BCR-ABL gene in chronic myeloid leukemia (CML). The transcriptional targets of Bcr-Abl in leukemic cells have not been extensively studied. A transcriptome experiment using the hematopoietic UT7 cell line expressing BCR-ABL, has identified the overexpression of eukaryotic elongation factor kinase 2 (eEF2K) which plays a major role in the survival of cells upon nutrient deprivation. Overall, the data suggest that overexpression of eEF2K in CML is associated with an increased sensitivity to nutrient-deprivation
Labrunie, Antoine. "Matériaux « uniques » pour cellules solaires organiques mono-composant." Thesis, Angers, 2017. http://www.theses.fr/2017ANGE0044/document.
Over the last few years, the development of bulk heterojunction organic solar cells (BHJ OSCs) led to significant increase in photovoltaic (PV) efficiency. Such devices are based on interpenetrated networks of an electron-donor material (D) and an electron-acceptor material (A) constituting the active layer. Nevertheless a careful optimization of the morphology is required to reach high power conversion efficiency. Furthermore, this optimized morphology can evolve towards spontaneous phase segregation which can be detrimental for the PV performances. To circumvent these limitations, a relatively unexplored approach relies on the use of a material where the donor and the acceptor moieties are covalently linked to each other through a nonconjugated π-connector. In this context, the work reported herein describes the synthesis and characterization of various molecular D-σ-A assemblies, as well as their preliminary evaluation as “unique” material for the realisation of single component organic solar cells (SC-OSCs). A first family of dyads and triads, based on quaterthiophene moieties as donor block, was studied. A general methodology to assemble the two D and A blocks via a Huisgen-type click-chemistry is described. Then, in the next chapters, several dyads based on a “push-pull” donor block have been synthesized and characterized. The PV performances of these compounds have been evaluated in SC-OSCs leading to power conversion efficiency up to 1.4 %, a value close to the state of the art
Geisler, Hubert. "Structuration d'hydrogels thermoactivables pour l'analyse de cellules uniques." Electronic Thesis or Diss., Université Paris sciences et lettres, 2020. http://www.theses.fr/2020UPSLS001.
We present in this work a new microfluidic technology aiming at isolating single cells by the use of thermoactuable polymers. One of the polymers we use is polyNIPAM, a polymer that can expand its volume by 400% in water when the temperature is set under 32°C and can shrink down when it is set over 34°C. We use this reversible swelling capability to open and close compartments embedded in a microfluidic chip.Grafting and structuring these hydrogel features relies on thiol-en click chemistry, initiated thermally or by UV irradiation. We have developed methods and microfabrication protocols in order to diversify the substrate materials (from glass to PDMS, COC, PMMA, etc), to expand the structures thickness range (from few microns to a tenth of microns) and to strengthen our knowledge regarding the fabrication impact on the hydrogel’s behavior. A robust protocol of photolithography has finally been worked on allowing the design of any type of 2D features on a large choice of substrates.One of the realistic applications detailed here is the development of microfluidic chips aiming at isolating single cells in hydrogel compartments. (confidential)
Vianay, Benoit. "Adhérence de cellules uniques sur supports micro-structurés." Phd thesis, Grenoble 1, 2009. http://www.theses.fr/2009GRE10329.
The cell adhesion is a critical process involved in many fundamental biological phenomena as dierentiation, tissue repair or cell development. This thesis focuses on a study combining experiments and modelization of single cells spreading on micro-fabricated substrates. Experimental results show that the geometrical constraint imposed by the adhesiveness contrast limits the adhesion. Beyond this limitation, a reproducible organization of the actin cytoskeleton of cells spreading on micro-structured materials suggests that simple physical laws govern the process. We have developed a classication method of basic geometrical shapes observed experimentally to obtain robust statistics. Based on the Cellular Potts model, we reproduced experimental results. This energetical model shows that the basic shapes are metastable states used by cells during spreading. The model parameters are linked to relevant biological parameters. We present results that connect the curvature of interfaces to biological parameters. We show that the experimental measurement of this curvature represents the competition between the contractility of stress bers and the elasticity of the actin gel. A correspondence between the physical properties in the model and the biochemical processes that regulate and organize the cellular adhesion is possible
Vianay, Benoit. "Adhérence de cellules uniques sur supports micro-structurés." Phd thesis, Grenoble 1, 2009. http://tel.archives-ouvertes.fr/tel-00455350.
Lu, Cong. "Analyse microélectrochimique du stress oxydant à l'échelle de la cellule unique : application aux cellules cancéreuses du sein." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2012. http://tel.archives-ouvertes.fr/tel-00828217.
Woringer, Maxime. "Tools to analyze single-particle tracking data in mammalian cells." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS419.
This work aims at providing tools to dissect the regulation of transcription in eukaryotic cells, with a focus on single-particle tracking of transcription factors in mammalian cells. The nucleus of an eukeryotic cell is an extremely complex medium, that contains a high concentration of macromolecules (DNA, RNA, proteins) and other small molecules (ATP, etc). How these molecules interact with transcription factors, and thus influence transcription rates is an area of intense investigations. Although some of these interactions can be captured by regular biochemistry, many of them, including weak, non-covalent interactions remain undetected by these methods. Live-cell imaging and single-particle tracking (SPT) techniques are increasingly used to characterize such effects. The inference of biophysical parameters of a given transcription factor (TF), such as its diffusion constant, the number of subpopulations or its residence time on DNA, are crucial to understanding how TF dynamics and transcription intertwine. Accurate and validated SPT analysis tools are needed. To be used by the community, SPT tools should not only be carefully validated, but also be easily accessible to non-programmers. They should also be designed to take into account known biases of the imaging techniques. In this work, we first propose a tool, accessible through a web interface, based on the modeling of the diffusion propagator. We validate it extensively and show that it exhibits state-of-the art performance. We apply this tool to two experimental settings: (1) the study of catalysis-enhanced diffusion in-vitro and (2) the analysis of the dynamics of the c-Myc transcription factor in mammalian cells
Foulon, Sophie. "Développement du séquençage ARN ciblé sur cellules uniques en microfluidique de gouttes et applications." Thesis, Paris Sciences et Lettres (ComUE), 2019. http://www.theses.fr/2019PSLET037.
Single cells technologies were introduced a few years ago and have been dramatically evolving ever since. These technologies have revolutionized biology, making it possible to better understand how heterogeneous cell systems works. For example, they permit to discover and follow cell subtypes, with applications in oncology or neurobiology. We have developed a technology to study the expression profile of genes of interest at the level of a single cell, using droplet-based microfluidics. By limiting the number of genes studied compared to commercial whole-transcriptome technologies, the targeted approach has several potential benefits: gaining deeper sequencing, increasing the number of cells studied, optimizing detection for low levels of expression, while reducing the complexity of data and costs. Targeting is sometimes essential, especially when the RNAs do not carry a generic primer sequence, as in the case of viral RNAs. Two applications are presented: the analysis of inflammation of the immune cells of the brain in the early stages of development, as well as the study of genetic recombination in the virus
Bontoux, Nathalie. "Analyse du transcriptome d'une cellule unique à l'aide d'une puce microfluidique." Paris 6, 2006. http://www.theses.fr/2006PA066600.
Tamra, Amar. "Spectroscopie diélectrique hyperfréquence de cellules individualisées sous électroporation." Thesis, Toulouse 3, 2017. http://www.theses.fr/2017TOU30011/document.
Electroporation is a physical process that consists in applying electric field pulses to transiently or permanently permeabilize the plasma membrane. This phenomenon is of great interest in the clinical field as well as in the industry because of its various applications, in particular electrochemotherapy which combines electrical pulses with the administration of a cytotoxic molecule in the treatment of tumors. The evaluation of this phenomenon is raditionally carried out using optical and biochemical methods (microscopy, flow cytometry, biochemical test). They are very effective but require the use of a wide range of fluorochromes and markers, which can be laborious and costly to implement, while being invasive to the cells. In recent years, the development of new biophysical tools for the study of electroporation has taken place, such as dielectrophoresis and impedance spectroscopy (low frequency). In addition to the ease of implementation, these methods are of interest in the study of membrane modifications of the cell. Hence the advantage of operating beyond the GHz, in the range of microwaves, for which the cytoplasmic membrane becomes transparent and the intracellular content is exposed. The extraction of the relative permittivity as a result of the electromagnetic field / biological cell interaction then reflects the cell state. This technique, microwave dielectric spectroscopy, is a relevant method for analyzing the effects of electroporation on cell viability. Moreover, it does not require any use of the exogenous molecules (non-invasive) and the measurements are directly carried out in the culture medium of the cells. Two objectives were defined during this thesis whose work is located at the interface between three scientific fields: cellular biology, microwave electronics and micro-technologies. The first objective concerns the transposition of conventional electroporation to the micrometric scale, which has shown an efficiency as efficient as the first. The second part of the work concerns the study by HighFrequency dielectric spectroscopy of cells subjected to different electrical treatments (combined or not with a cytotoxic molecule). This work presents a statistical power and shows a very good correlation (R2> 0.94) with standard techniques used in biology, which biologically validates the HF analysis method in the context of electroporation. This work also shows that microwave dielectric spectroscopy proves to be a powerful technique capable of revealing cell viability following chemical and / or electrical treatment. They open the way to 'non-invasive' analysis by hyper-frequency dielectric spectroscopy of electroporated cells in situ
Lombard, Alain. "QuanTI-FRET, un outil d'imagerie pour l'analyse de la mécanotransduction dans les cellules vivantes uniques." Thesis, Université Grenoble Alpes, 2020. http://www.theses.fr/2020GRALY055.
Many elementary cellular processes (migration, differentiation, death) are controled by a set of agents linked together by cascade reactions. Some of these signaling networks convert mechanical signals external to the cell into internal biochemical signals, a process called mechanotransduction. We seek to study these networks through a signal processing approach, in order to experimentally determine an analogous of the transfer function in time and space for mechanotransduction.Controlling the input variable is done by different type of 2D substrates which have been developped, from the simple glass surface, the adherent geometrical patterns, to the magneto-active substrates (composed of micro-pillars inserted into an elastomer) capable of stimulating locally and dynamically the cells.Measuring the biochemical output variable is done by FRET biosensors. The fluorescence emitted is collected through an inverted widefield fluorescence microscope. We set up the quantitative FRET efficiency calculus from this fluorescence without using FRET standards. It gives access to the activity in space and time of some molecules of network signalisation.Some tools are finally presented as potential candidates to perform the transfer function, among them are combination of correlation methods, and singular value decomposition used in acousto-optics. Combiantion of these tools and methods remains complex, particularly to highlight a biological behaviour from a quantitative quantity. The first use of these tools do not give any biological result, but are promising to study mechanotransduction
Traboulsi, Abdel-Meneem. "Étude à moyen-débit de la localisation d'ARNm dans les cellules humaines." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT117.
MRNA localization was discovered in 1983 in ascidian oocytes and early embryos. Since then many examples of localized RNAs have been found in many organisms, including plants, yeast, fungi, insects, fish and mammals. Localized mRNAs contribute to many biological functions, such as embryonic patterning, asymmetric cell division, cell migration, signaling, neuronal plasticity and others…Until now, only few studies analyzed RNA localization in a systematic manner. Three of them were done in Drosophila, during embryogenesis, oogenesis or larval stage and analyzed around 16000 mRNAs in total. The two other studies were done in mammalian cells and analyzed nearly 1000 mRNAs each. These studies opened a door and raised questions regarding the importance of mRNA localization in human cells and its implication in different biological processes. The goal of my thesis was thus to increase the throughput of single molecule FISH techniques (smFISH) and to study mRNA localization in HeLa cells in a systematic manner.One limitation in smFISH is the cost of the fluorescent oligonucleotide probes, which limits the number of mRNAs that can be analyzed. Therefore, I developed an alternative protocol in which probes for many genes were synthesized as a pool of oligonucleotides (40 per gene in average, more than 12000 in total). Gene-specific probes were then amplified by PCR and converted into single strand by in vitro transcription. I generated a complete protocol, starting from probe design and up to image acquisition. I was interested in studying cell cycle genes. Indeed, cell cycle genes have been extensively studied at the protein level but little is known concerning the localization of their mRNAs. During mitosis, cells go through important morphological modifications and local translation could be a mean of achieving protein localization. This screen is ongoing.In parallel to these experiments, I performed a smFISH based screen on 100 randomly chosen genes and 50 regulators of the G2/M transition of the cell cycle, using a traditional smFISH protocol. In this set-up, I took advantage of a library of HeLa cell lines, in which each cell line contains a bacterial artificial chromosome with the gene of interest tagged with GFP. Therefore, using oligonucleotides hybridizing to the GFP sequence, I could use the same probe set to study the localization of all the tagged mRNAs. A further advantage is that protein localization could be assessed simultaneously. My results indicate that two mRNAs showed a specific localization when screening 100 random genes, and 16 mRNAs among the 50 regulators of the G2/M transition. These mRNAs belong to five localization classes: "blobs", which are cytoplasmic mRNA aggregates; "clusters", which are areas of high local mRNA concentration but where individual mRNA can still be resolved; "nuclear envelope", where mRNAs concentrate around the nuclear envelope; "spindle", which are mRNAs accumulating on the cell division apparatus during mitosis, “spots" which are cytoplasmic mRNA aggregates where individual mRNA can’t be resolved and are bigger than blobs. Interestingly, colocalization between mRNA and GFP, which suggests local translation, was only found for 1 mRNA.These random and targeted screens performed at small-scale show an unexpected frequency and diversity in mRNA localization patterns, therefore pointing to new functions related to this process. This will stimulate future studies aiming at performing screenings at a higher scale
Meistermann, Dimitri. "Modélisation du développement préimplantatoire humain à partir de données de transcriptome de cellule unique." Thesis, Nantes, 2020. http://www.theses.fr/2020NANT1019.
Ce travail de thèse est consacré à l’étude de nouveaux mélanges gazeux pour la gravure plasma du CdHgTe, à savoir : CH₃NO₂/H₂/Ar, CH₃OH/H₂/Ar et CH₄/NO₂/H₂/Ar. L’objectif est de graver sans polarisation du substrat pour limiter l’énergie déposée sur les surfaces gravées. Une première partie portant sur l’analyse de ces plasmas par sondes électrostatiques et spectroscopie d’émission optique a permis de montrer que la substitution de nitrométhane ou méthanol au méthane a un effet sur la composante chimique de la gravure. Pour ces nouveaux mélanges hydrocarbonés, l’apparition de molécules telles que CO et CN est corrélée à l’annihilation du dépôt spontané de polymère. La seconde partie, consacrée à la gravure du CdHgTe avec ces nouveaux précurseurs a prouvé la faculté de graver sans polarisation du substrat avec les mélanges CH₃NO₂/H₂/Ar et CH₄/N₂O/H₂/Ar et ainsi réduire les dommages engendrés au matériau, notamment la rugosité en surface. Une étude plus poussée de la gravure en mélange CH₄/N₂O/H₂/Ar montre notamment une augmentation de la vitesse de gravure pour les faibles polarisations jusqu’à un certain seuil, avant qu’elle ne stagne, correspondant au passage d’une gravure à dominance chimique à une gravure à dominance physique. De plus, la rugosité est indépendante de la puissance d’excitation du plasma, de la température du substrat ainsi que de la durée de gravure. Enfin, la gravure de tranchées a permis de mettre en évidence la gravure chimique et isotrope à faible polarisation avec les mélanges CH₄/N₂O/H₂/Ar et CH₃NO₂/H₂/Ar mais qui, à plus forte polarisation présente une meilleure passivation latérale que les gravures en plasma CH₄/H₂/Ar
Ben, Meriem Zacchari. "Memory of stress response in the budding yeast Saccharomyces cerevisiae." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC311.
Cellular memory is a critical ability displayed by micro-organisms in order to adapt to potentially detrimental environmental fluctuations. In the unicellular eukaryote S. cerevisiae, it has been shown at the population level that cellular memory can take the form of a faster or a decreased response following repeated stresses. We here present a study on how yeasts respond to short, pulsed hyperosmotic stresses at the single-cell level. We analyzed the dynamical behavior of the stress responsive STL1 promoter fused to a fluorescent reporter using microfluidics and fluorescence time-lapse microscopy. We established that pSTL1 displays a dynamical variability in its successive activations following two short and repeated stresses. Despite this variability, most cells displayed a memory of past stresses through a decreased activity of pSTL1 upon repeated stresses. We showed that this memory does not require do novo protein synthesis. Rather, the genomic location is important for the memory since promoter displacement to a pericentromeric chromatin domain leads to its decreased transcriptional strength and to the loss of the memory. Interestingly, our results points towards an unreported involvement of the SIR complex on the activity of pSTL1 only when displaced to the pericentromeric domain in our experimental conditions. This study provides a quantitative description of a cellular memory that includes single-cell variability and points towards the contribution of the chromatin structure in stress memory. Our work could serve as a basis to broader studies on the positioning of stress response genes at subtelomeric positions in the budding yeast, from a genetic point of view as well as an evolutionary one
Nattes, Tristan de. "Rejet humoral d'allogreffe rénale et allo-immunisation HLA." Electronic Thesis or Diss., Normandie, 2023. http://www.theses.fr/2023NORMR053.
Kidney transplantation is the best treatment of end-stage renal disease, improving life quality and quantity. Despite advances in pathophysiological knowledge of kidney transplant immunology, kidney transplant rejection remains the major cause of allograft dysfunction, especially antibody-mediated rejection.Antibody-mediated rejection risk assessment is based on the evaluation of donor-specific anti-HLA antibodies. However, these antibodies have a poor predictive value for incidence and prognosis of rejection. This could be explained by the heterogeneity of their intrinsic characteristics. These characteristics depend on cells responsible for their secretion, which include short- and long- lived plasma cells. Consequently, they indirectly depend on the cells responsible for maintaining the pool of these antibody-secreting cells, such as memory B cells. In infectious diseases, it is known that memory B cells are heterogeneous in terms of phenotype, function, degree of clonality, and diversification of their B-cell receptor (BCR). However, this heterogeneity has not been examined in the context of kidney transplantation.The aim of the first part of this thesis was to study the heterogeneity of HLA-specific memory B cells in sensitised patients on kidney transplant waiting list. To this end, single-cell analysis of HLA-specific memory B cells from patients with various aetiologies and degrees of immunisation was performed. This led to their phenotypic and transcriptomic characterisation and to the assessment of their BCR repertoire.The second part of this thesis was dedicated to the diagnosis of kidney transplant rejection.In recent years, biopsy-based transcriptomics has emerged, enabling the assessment of hundreds of transcripts in kidney biopsy tissue. These tools provide the opportunity to elucidate new physiopathological pathways and potentially enhance the diagnosis of rejection, especially humoral rejection. However, their application in clinical practice is still limited due to their restricted availability, required expertise for data processing and interpretation, and cost. Furthermore, their exact impact on patient management remains undetermined. Here, a molecular diagnostic tool with characteristics suitable for clinical use was developed. This tool enables the diagnosis of rejection and its classification between antibody-mediated and T-cell mediated rejection. Subsequently, this tool was assessed in ambiguous clinical situations to evaluate its impact in clinical practice.Through these studies, this thesis focused on enhancing our understanding of the humoral response in renal transplantation, which could help improving immunological risk stratification in transplantation. Additionally, it aimed to improve biopsy-based transcriptomics in the diagnosis of kidney transplant rejection
Calvez, Vincent. "Modèles et analyses mathématiques pour les mouvements collectifs de cellules." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2007. http://tel.archives-ouvertes.fr/tel-00255811.
Dans une première partie nous étudions plusieurs variantes du modèle PKS classique, incluant notamment une diffusion non-linéaire des cellules, ou bien une loi de diffusion chimique à noyau de Green logarithmique. Puis nous montrons l'existence globale pour une masse sous-critique du modèle PKS classique dans tout l'espace $\mathbb{R}^2$.
On complexifie ensuite le modèle de base en ajoutant un intermédiaire chimique réactionnel, ce qui modifie l'homogénéité du système. Enfin les conditions d'existence globale pour le modèle cinétique ODA avec effets délocalisants sont affaiblies par rapport aux travaux précédents.
Dans une deuxième partie nous appliquons le modèle phénoménologique de PKS, et son principe de masse critique, à un processus d'auto-organisation remarquable dans le cerveau: la sclérose concentrique de Baló. Un couplage adéquat entre un front de propagation et une instabilité de PKS décrit raisonnablement les motifs en anneaux de la maladie.
La troisième partie adopte le point de vue du transport optimal de masse pour analyser le modèle de PKS unidimensionnel modifié auparavant (afin de partager les caractéristiques de PKS 2D). Bien que la fonctionnelle d'énergie ne soit pas convexe par déplacement, nous démontrons la convergence vers un unique état d'équilibre, lorsqu'il existe. Ces nouvelles idées sont mises en oeuvre numériquement~: un flot gradient discret pour la distance de Wasserstein est analysé, puis simulé en dimension un d'espace.
Plusieurs annexes viennent compléter ce travail, dont une annexe qui regroupe tous les aspects numériques de la thèse.
Parutto, Pierre. "Statistical analysis of single particle trajectories reveals sub-cellular nanodomain organisation and function." Thesis, Paris Sciences et Lettres (ComUE), 2019. http://www.theses.fr/2019PSLEE055.
Single-Particle Trajectories (SPTs) obtained from super-resolution microscopy allow to track proteins with nanometer precision in living cells and are used in neuroscience and cellular biology. In this thesis, I was interested in the high-density nanodomains found in these trajectories that can be modeled as potential wells. To characterize them, I developed a new hybrid method based on the point density and local drift field and compared it to the other state-of-the-art methods. Then, I used it to identify transient potential wells in SPTs of voltage-gated calcium channels (CaV) contributing to a better understanding of the role of the different CaV splice variants in synaptic transmission. In another study, I looked at SPTs from Endoplasmic Reticulum (ER) luminal resident proteins where I developed a method to reconstruct the network from trajectories and used it to characterize the luminal motion as a jump-diffusion process, which allows for a better redistribution of the luminal content than the previously assumed diffusive model. Finally, I discuss other analyses of motions for lysosome-ER interactions, CaV2.1 channels at drosophila’s neuromuscular junctions and the description of the motion of the constituent proteins of the NuRD chromatin remodeling complex
Dufour, Adrien. "Déchiffrer le réseau moléculaire contrôlant la pluripotence du porc." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL035.
Current global changes are forcing us to rethink our production systems and the way we select and phenotype animals. The use of pluripotent stem cells capable of self-renewal and differentiation into a multiplicity of cell types is an asset that will make it easier to assess phenotypes that are difficult to measure in livestock farming. To improve our knowledge of the biology of porcine pluripotent cells, I carried out a transcriptome analysis at the single-cell level on porcine embryos. This analysis enabled me to identify new cellular subpopulations in extra-embryonic tissues, to highlight signalling pathways and cellular interactions specific to each population, and to link them to gene regulation modules. Based on these data and the literature, we were able to develop a culture medium for the amplification and maintenance of porcine embryonic stem cells (pESC). I then carried out a transcriptome and epigenome analysis at cell level on porcine embryos and our pESC lines, enabling me to establish the link between epigenetic and transcriptional differences between embryonic populations and to study their evolution during development. I was also able to compare the phenotype of pESCs with the epiblast of the porcine embryo, which enabled me to identify their differences and similarities in terms of signalling pathways and gene regulation modules. I also identified two subpopulations in the ESC lines with specific epigenetic signatures and gene regulatory modules. Taken together, these results highlighted the importance of cell-cell interactions for embryo development and pluripotent cell biology, and identified new gene regulatory modules associated with pluripotency. Finally, the identification of two pluripotent cell subpopulations in our cultures raises the question of the heterogeneity of these cell lines and the possible consequences for their fate and potential
Martineau, Eugénie. "Linking single cell directionality to dynamic multicellular transitions in Myxococcus xanthus : a multiscale analysis." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0089.
The δ-proteobacteria Myxococcus xanthus has been a model of study for decades for its self-organized behavior as a response of environmental stimuli. It colonizes favorable ecological niches by using surface motility. In particular, this motility allows M.xanthus to predate collectively over prey microorganisms, while under starvation they start a developmental process to form macroscopic fruiting bodies, filled with environmental resistant myxospores. All these multicellular behaviors require a dynamic control of the cell polarity established by the polarity proteins MglA, MglB and RomR. Together, they define the direction of movement of the cell, which can be rapidly inverted by the Frz chemosensory system (reversion). In this thesis work, through combined computational/experimental approaches, we highlight that the regulation system forms a new type of biochemical oscillator, controlled by two proteins RomR and FrzX, which act together through complementary action to trigger the reversion at the lagging pole. The unique architecture of this system allows a wide response to various stimuli, which could be very beneficial for collective cell behaviors. To understand the importance of these transitions, we have developed a new high-resolution single cell assay linking single cMARTINEAU EUGENIE 2018AIXM0089/016ED62 2018/03/21 62 SCES SCHell behaviors to multicellular structures at unprecedented spatial and temporal resolutions. This way, we have investigated the role of the newly identified biochemical oscillator in the multicellular model of predation
Bost, Pierre. "Decoding cellular communications and interactions between immune cells by using single-cell approaches." Electronic Thesis or Diss., Sorbonne université, 2020. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2020SORUS020.pdf.
Cellular communications are essential to the proper functioning of multi-cellular organisms, particularly in order to adapt to a constantly changing environment. The cells of the immune system are no exception to this rule, but the interactions between immune cells remain little known and complicated to study. The recent emergence of 'single cell' sequencing technologies represents a unique opportunity to study these communications. In this thesis, different experimental and analytical approaches have been developed to study these communications on a single cell scale. These strategies were then applied to different disease contexts, including COVID-19, Alzheimer's disease or immunisation with inactivated pathogens, and identified previously unknown or poorly understood cellular communication pathways. However, the effectiveness of these approaches is limited by the lack of information on cell location and further work integrating such data will be essential to go further in the dissection of immune cell communications
Crozatier, Cécile. "Contrôle et analyse électrochimique de la réactivité biologique à l'échelle de la cellule unique dans un dispositif microfluidique." Phd thesis, Université Paris-Diderot - Paris VII, 2007. http://tel.archives-ouvertes.fr/tel-00178656.
Grâce au développement d'outils modulables de culture cellulaire et de manipulation de cellules vivantes dans des dispositifs microfluidiques, nous avons mis en place le contrôle dynamique stable de stimulations chimiques sur une population de cellules souches mésenchymateuses (CSM) en culture et poursuivons cette étude dans le but d'induire la réactivité cellulaire des CSM vers la voie de différenciation neuronale.
Le développement d'un microsystème intégré de détection électrochimique du stress oxydant sur cellules uniques est mis en oeuvre à travers la réalisation d'un dispositif microfluidique intégré consistant en un réseau de chambres de mesures, contenant des microélectrodes fonctionnelles, et permettant d'isoler des macrophages uniques et de les maintenir en survie pendant plusieurs dizaines de minutes, durée suffisante pour réaliser nos mesures électrochimiques. En faisant varier les conditions de mesure, comme le nombre de cellules sondées dans le même micro-environnement, la nature du stimulus ou la présence ou non de communication cellulaire avec une population voisine, nous posons les bases d'une analyse originale jamais réalisée jusqu'à présent.
Robert, Michèle. "Etude quantitative des constituants épithéliaux et mésenchymateux dans l'hypertrophie bénigne de la prostate : comparaison des résultats obtenus sur pièces d'adénomectomie et biopsies uniques et multiples." Montpellier 1, 1995. http://www.theses.fr/1995MON1T038.
Eisele, Almut. "La cinétique de différentiation des cellules souches hématopoïétiques uniques après transplantation : l´état d´équilibre et l´effet de la cytokine érythropoïétine." Thesis, Paris Sciences et Lettres (ComUE), 2019. https://tel.archives-ouvertes.fr/tel-03028817.
Hematopoietic cells are the most numerous cells in our body, and their overall short half-life requires their steady production. At the apex of the hematopoietic system resides a small number of hematopoietic stem cells (HSC) which give rise to all mature hematopoietic cell types through self-renewal and differentiation divisions. For long it was assumed that these HSC are a homogeneous population of multipotent cells. Technical advancements, which allowed to trace HSC at the single cell level, revealed however that single HSC behave differently with respect to the number of lineages and the relative amounts of different lineages they produce and are heterogeneous with respect to their long-term engraftment capacity. Notably different lineage restricted and biased cells, as well as cells with long-term and short-term engraftment potential have been identified in the HSC gate. One technique allowing the lineage tracing of single HSC is cellular barcoding, which relies on the introduction of an artificially created DNA fragment, the barcode, in the genome of HSCs through viral transfection. As these barcodes are transmitted to all daughter cells, the analysis of the barcode identity of progeny cells reveals which lineages and how much of each is produced by each individual HSCs.In this thesis we used a new cellular barcoding library to analyze how the different HSC subsets previously described interact and behave in the first six weeks after bulk transplantation, as well as the influence of erythropoietin (EPO) on this process. More in detail, we described the reconstitution kinetics of HSC in the myeloid (M; macrophage, monocytes, neutrophils, eosinophils), lymphoid (B-cells), dendritic cells, megakaryocyte and erythroid lineage (E; erythroblasts) at the single cell level. For the analysis of HSC differentiation towards the erythroid lineage we established the detection of cellular barcodes from RNA. We discovered that HSC clonal succession and clonal stability co-occur in the first weeks after transplantation, but are not evenly distributed over the different hematopoietic lineages. Notably the production of erythroid cells 2-weeks after transplantation was maintained by distinct short-lived HSC clones, while high myeloid cell production after transplantation was guaranteed by long-lived multi-outcome HSCs. In vitro EPO exposure of HSC before transplantation, did not change the overall lineage output of transplanted HSC, or HSC differentiation kinetics, lineage restrictions, and biases at the single cell level in the first six weeks after transplantation. However, after transplantation of EPO-exposed HSC long-lived unbiased multi-outcome HSCs lost preponderance with respect to cellular output. Rather, changing clones of two types of highly biased HSCs, myeloid-erythroid (ME)-biased and myeloid B-cell (MB)-biased HSC, produced now the majority (>60%) of erythroid, myeloid and B-cells. This effect was transient but stable over different EPO concentrations and after in vivo EPO treatment during transplantation. It suggests a functional compensation mechanism at work.We hope the detailed description of the engraftment kinetics of single control and EPO-exposed HSC after bulk transplantation will have relevance both for fundamental research and the clinics
Chabert, Max. "MICROFLUIDIQUE DE GOUTTES POUR LES ANALYSES BIOLOGIQUES." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2007. http://tel.archives-ouvertes.fr/tel-00180994.
Dans une première partie, nous décrivons la conception d'un système permettant d'effectuer en flux et sans contamination la réaction de PCR dans des microgouttes transportées par une huile immiscible. Cette étude a débouché sur une plateforme automatisée au débit théorique de 3000 échantillons par jour, égalant les systèmes actuels avec une consommation 50 fois moindre en réactifs.
Dans les parties suivantes, nous présentons deux nouvelles idées pour la manipulation d'objets en microfluidique digitale : l'utilisation de phénomènes hydrodynamiques pour encapsuler des cellules uniques dans des microgouttes et les trier, et l'application de champs électriques pour induire mélange et coalescence de gouttes aqueuses. La combinaison de ces deux méthodes au sein d'une même puce est le premier pas vers un système intégré d'analyse de cellules uniques.
Chen, Wenli. "Spectroscopie diélectrique hyperfréquence de cellules uniques cancéreuses : de l'optimisation du capteur en sensibilité et répétabilité jusqu'au suivi en temps réel de stimuli chimiques." Thesis, Toulouse 3, 2016. http://www.theses.fr/2016TOU30219/document.
The measurement of biological cells is a routine step in many biological investigations. Current techniques used by biologists are mainly based on staining or fluorescent labelings, which provide very precise and effective molecular and cellular observations. Within this context, the microwave dielectric spectroscopy for cell analysis represents a new and attractive method, due to the lack of cells preparation and manipulation, without adding chemicals that could interfere with other cellular constituents. Its compatibility with the analysis of single-cells, potentially in real-time monitoring, constitute also two major assets of the analysis technique. This PhD thesis therefore focused on the optimization of a microfluidic and microwave based biosensor, which is dedicated to the dielectric spectroscopy of individual biological cells, and the development of its metrology to assess the dielectric behavior of cells subjected to chemical stimuli. After a state of the art on the current techniques available to analyze single cells, we focused on the optimization of the microwave biosensor to improve its performances in terms of sensitivity and repeatability. These optimizations dealt with the microfabrication process, the component architecture through the investigation of single cell loading efficacy as well as an electromagnetic parametric study. These developments were validated first experimentally with the measurement of polystyrene beads, which present a simplified dielectric model compared to the complexity of a biological cell, followed then by living individual cells in their culture medium. The test bench was also optimized to allow the dielectric measurement of cells over time, and especially in response to a chemical stimulus. The reaction kinetics of a single-cell subjected to saponin was recorded automatically for different cells. This work opens the door to single-cell analysis with microwave dielectric spectroscopy of complex biological processes in real-time
Uwizeye, Clarisse. "Approches quantitatives d’imagerie pour explorer les cellules photosynthétiques." Thesis, Université Grenoble Alpes, 2020. http://www.theses.fr/2020GRALV043.
Phytoplankton is the group of photosynthetic microorganisms (microalgae and cyanobacteria) living in suspension in marine and fresh waters. Through photosynthesis, phytoplankton produce large amounts of the oxygen essential for marine and terrestrial life. Marine microalgae are also promising organisms for biotechnological applications (human and animal food, biofuels). Because of their ecological and economic importance, the study of the phytoplankton responses to environmental challenged (including the ones induced by human activity and global warming) is a developing field of research. Phytoplankton activity is influenced by changes in the vertical stratification of the water column, which modulate light energy availability as well as nutrient supply to phytoplankton cells in a temperature-dependent manner. Based on light and nutrient availability, phytoplankton cells have evolved different lifestyles: autotrophy (photosynthetic activity), mixotrophy (simultaneous use of photosynthesis and respiration of exogenous carbon sources for growth) and photosymbiosis (symbiotic interactions with animal cells).In this thesis, I have studied the physiological responses of phytoplankton cells to environmental changes at the cellular and subcellular levels. To achieve this goal, I have developed a complete imaging workflow to perform quantitative morphometric analyses of entire algal cells, representatives of ecologically-successful and laboratory-model microalgal species. The protocol starts with FIB-SEM (Focused Ion Beam - Scanning Electron Microscopy) or SBF-SEM (Serial Block Facing – Scanning Electron Microscopy), to acquire high-resolution images. By implementing the 3D image analysis protocol, it is possible to obtained high-resolution whole cells models in three dimensions, suitable to perform quantitative analyses. Thanks to these tools, I have been able to image the adaptation of phytoplankton to various environmental conditions: i. changes in the size and morphology of plastids and mitochondria during light acclimation in diatoms, ii. changes in organelles interaction during nutrient acclimation in Nannochloropsis, iii. morphological changes occurring during photosymbiosis in Phaeocystis.Overall, this work reveals several scenarios of phytoplankton acclimation at both the cellular and subcellular levels. I have also validated the use of this protocol in plants in a study on chloroplast biogenesis during de-etiolation in Arabidopsis. of plastids
Soule, Pierre. "Etude des mécanismes de translocation des peptides pénétrateurs de cellules (cpp) à l'aide de techniques biophysiques." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066563/document.
Gene therapy relies on an efficient and specific delivery of drugs into targeted cells. For this purpose, the use of carriers that will help the drugs to cross the membrane, without introducing deleterious effect due to the membrane disruption, are promising. A family of such carriers is known as Cell Penetrating Peptides (CPPs). These peptides are short, about ten amino acids, and often cationic. They are able to translocate through the membrane with different cargos and deliver them into the cytosol. However the mechanisms are still, to a great extent, unknown. We used three biophysical techniques to gain insights into the mechanisms leading to the translocation of a CPP. i) We found the heparan sulfates to be the strongest partner of the CPP penetratin at the cell surface. This adhesion has been pointed out using the Biomembrane Force Probe, a force measuring tool. ii) We evidenced the translocation of penetratin through the lipid bilayer (without any cell mechanism) as long as it contains enough negatively charged lipids. This has been carried out using model bilayers formed at the interface between droplets generated by an inverted emulsion: water in an oil and lipid mixture. iii) To view the translocation of CPPs at the single molecule level we developed a total internal reflection fluorescence microscope (TIRFM) on a suspended bilayer
Koh, Alaric C. W. "Analyses électrochimiques d’espèces réactives de l’oxygène et de l’azote produites par un macrophage immunostimulé." Paris 6, 2009. http://www.theses.fr/2009PA066465.
Bonnaffoux, Arnaud. "Inférence de réseaux de régulation de gènes à partir de données dynamiques multi-échelles." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSEN054/document.
Inference of gene regulatory networks from gene expression data has been a long-standing and notoriously difficult task in systems biology. Recently, single-cell transcriptomic data have been massively used for gene regulatory network inference, with both successes and limitations.In the present work we propose an iterative algorithm called WASABI, dedicated to inferring a causal dynamical network from timestamped single-cell data, which tackles some of the limitations associated with current approaches. We first introduce the concept of waves, which posits that the information provided by an external stimulus will affect genes one-byone through a cascade, like waves spreading through a network. This concept allows us to infer the network one gene at a time, after genes have been ordered regarding their time of regulation. We then demonstrate the ability of WASABI to correctly infer small networks, which have been simulated in-silico using a mechanistic model consisting of coupled piecewise-deterministic Markov processes for the proper description of gene expression at the single-cell level. We finally apply WASABI on in-vitro generated data on an avian model of erythroid differentiation. The structure of the resulting gene regulatory network sheds a fascinating new light on the molecular mechanisms controlling this process. In particular, we find no evidence for hub genes and a much more distributed network structure than expected. Interestingly, we find that a majority of genes are under the direct control of the differentiation-inducing stimulus. Together, these results demonstrate WASABI versatility and ability to tackle some general gene regulatory networks inference issues. It is our hope that WASABI will prove useful in helping biologists to fully exploit the power of time-stamped single-cell data
Contreras, Vanessa. "Les cellules dendritiques de la lymphe pseudo-afférente cutanée chez le mouton : analyses fonctionnelles et transcriptomiques." Versailles-St Quentin en Yvelines, 2010. http://www.theses.fr/2010VERS0002.
Mouse spleen contains two DC subsets (CD8a+ and CD8a-). CD8a+ DC appear to be specialized in the uptake of dying cells, the IL-12 production, and the cross-presentation of exogenous antigens. Thus CD8a+ DC are targets for vaccine improvement. We showed that sheep CD26+ DC share a common transcriptomic signature and several common functions with the mouse CD8a+ DC. Moreover, CD26+ DC transport epithelium-derived cell remnants. As we could elute a cytokeratin peptide from the lymph DC MHC class II molecules, we suggest that the CD26+ DC can present self antigens from skin in the process of self tolerance. Finally, CD26+SIRP- and CD26- DC expressed different cytokine mRNA after activation with a recombinant adenovirus. In these studies, we showed that the DC subset organisation is conserved between several mammal species and we generated molecular data for the development of new vaccines, based on more efficient DC targeting
Duran, Nathalie. "La protéine EB2 du virus d'Epstein-Barr : activateur post-transcriptionnel : analyses structurales et fonctionnelles." Lyon 1, 1995. http://www.theses.fr/1995LYO1T173.
Cisbani, Giulia. "Cell replacement therapy for Huntington's disease : what we have learned from post-mortem analyses of grafted patients and mice models." Doctoral thesis, Université Laval, 2014. http://hdl.handle.net/20.500.11794/25302.
Huntington’s disease (HD) is a devastating autosomal dominant neurodegenerative disorder which manifests because of a mutation in the huntingtin gene. It is characterized by a variety of clinical signs which include psychiatric and cognitive problems as well as motor disabilities, in large part choreiform movements. Neuropathologically, the brains of patients afflicted with this disease present with a major atrophy of the cortex and striatum where massive cell losses are observed. To this day, cures remain unavailable and for this reason, an enormous amount of energy has been put into the development of experimental approaches, and for example into embryonic neuronal cell transplantation, which aims to replace lost cells. A few clinical trials have thus been initiated to evaluate whether such methodologies would be beneficial to patients. My PhD thesis focused, in large part, on the analysis of a number of brains from patients recruited for the University of South Florida trial and who eventually came to autopsy. These patients (4 analyzed post-mortem) received solid pieces of fetal striatal tissue and died between 9 and 12 years post-transplantation. Previous work carried out in Dr. Cicchetti’s laboratory has shown that graft survival is compromised in these patients long-term. The aim of my project was to further understand the mechanisms underlying this suboptimal graft survival. We hypothesized that 1) poor vascularization of the graft, 2) the method of transplantation (solid tissue vs. suspension cells) and 3) the potential presence of mutant huntingtin (mHtt) within the grafted tissue may all contribute to graft demise. Indeed, elements of the neurovascular unit were largely absent within the solid grafts. Grafts presented a lower density of capillaries and absence of large blood vessels compared to the host brain. Moreover, we observed a reduced number of astrocytes within the grafts and a limited interaction of these cells with blood vessels, suggesting impairment in blood brain barrier elements. The absence of astrocytes was accompanied by the lack of the gap junction subunit connexin 43, important for graft-host integration. Interestingly, when dissociated cells were transplanted in the striatum of YAC128 mice, a murine model of HD graft survival was excellent and neither the graft vascularization nor the interaction between astrocytes and vessels was altered. Finally, we describe for the first time the presence of mHtt inclusions within the grafted tissue. In the HD transplanted cases, aggregates were detected only in the extracellular matrix of the graft while in the host brain they co-localized with neurons or other cellular elements, such as the basal lamina of blood vessels. Taken together, this thesis sheds new light onto potential mechanisms contributing to poor long-term graft survival in HD patients. These results will help improve such therapies as well as to better understand disease process in HD.
Aquino, Yann. "Bases génétiques et évolutives de la variabilité interpopulationnelle de la réponse immunitaire au SARS-CoV-2." Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS488.
Humans display substantial interindividual clinical variability after SARS-CoV-2 infection, the genetic and immunological basis of which has begun to be deciphered. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells—from 222 healthy donors of diverse ancestries—that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk
Bertin, Benjamin. "Analyses moléculaires et fonctionnelles de la diversification musculaire par de nouvelles approches génomiques cellules-spécifiques chez la drosophile." Thesis, Université Clermont Auvergne (2017-2020), 2017. http://www.theses.fr/2017CLFAS002/document.
Skeletal muscles display specific features (size, shape, orientation, attachment site,number of nuclei), which are tightly controlled by the combinatorial expression of identity factors. Currently, process by which identity genes determine muscle characteristics is not fully understood. Uncovering how identity factors are interconnected and how they control network of genes specifying muscle cell fate remains a major challenge. To discover new actors of the identity code allowing the acquisition of individual muscle characteristics during Drosophila embryogenesis we optimised a genome wide cell specific approach called TRAP (Translating Ribosome Affinity Purification), which allows the isolation of mRNA engaged in translation. This method has been used on two restricted populations of muscle cells (Slou and Lms positive) and on the global musculature (Dufpositive) at three time windows covering key muscle developmental steps such as founder cell specification, myoblast fusion, attachment to the epidermis via tendon cells and the innervation by motoneurons.To assess gene expression at a global level in these muscle subsets, we performed transcriptomic analyses at targeted developmental windows by using microarray. First, a comparison of spatial gene expression allowed us to identify new potential actors of the identity code for Slou-positive muscles and the involvement of the RNA binding protein Bol in the structural organisation of muscle fibers. We also performed analyses of temporal transition profiles of genes differentially expressed in Slou- and Lms-positive muscles and identified cluster of genes enriched preferentially in the Lms population and encoding actin interacting proteins. We focused on two genes from this cluster, gel and dCryAB and determined their functions during myogenesis. These two proteins control a coordinated growth of the Lms-positive muscles by fine-tuning of both the number of fusion events and the elongation of myotubes to tendon cells. With this project, we have identified new potential actors of the identity code that govern the acquisition of individual properties of Slou and Lms muscle subsets during Drosophila embryogenesis. We hope that the newly generated data will enable to gain further knowledge on the corresponding orthologues during vertebrate myogenesis and will help to understand why particular muscles are affected in some myopathies
Ozier-Lafontaine, Anthony. "Kernel-based testing and their application to single-cell data." Electronic Thesis or Diss., Ecole centrale de Nantes, 2023. http://www.theses.fr/2023ECDN0025.
Single-cell technologies generate data at the single-cell level. They are coumposed of hundreds to thousands of observations (i.e. cells) and tens of thousands of variables (i.e. genes). New methodological challenges arose to fully exploit the potentialities of these complex data. A major statistical challenge is to distinguish biological informationfrom technical noise in order to compare conditions or tissues. This thesis explores the application of kernel testing on single-cell datasets in order to detect and describe the potential differences between compared conditions.To overcome the limitations of existing kernel two-sample tests, we propose a kernel test inspired from the Hotelling-Lawley test that can apply to any experimental design. We implemented these tests in a R and Python package called ktest that is their first useroriented implementation. We demonstrate the performances of kernel testing on simulateddatasets and on various experimental singlecell datasets. The geometrical interpretations of these methods allows to identify the observations leading a detected difference. Finally, we propose a Nyström-based efficient implementationof these kernel tests as well as a range of diagnostic and interpretation tools
Rolland, Delphine. "Apport des analyses globales dans les lymphomes B : recherche d'anomalies moléculaires pour un ciblage thérapeutique." Lyon 1, 2008. http://www.theses.fr/2008LYO10216.
Lymphomas are incurable neoplasia, especially mantle cell lymphoma (MCL), marginal zone lymphoma (MZL) and small lymphocytic lymphoma (SLL). In our study, we tried to identify new therapeutic targets using 2 different approaches. First, based on the overexpression of their transcripts, two molecular abnormalities were evaluated as potential therapeutic targets in MCL: GST-π and FTase. In vitro, the GST-π nuclear transfer inhibition increased the cytotoxic activities of several drugs. In vitro, the FTase inhibition by tipifarnib induced cell growth arrest, apoptosis and displayed synergistic effects with drugs used in MCL therapies. In MCL xenograffed mice tipifarnib has shown cytostatic activity. In a multicentric clinical phase II study, 1 of 11 patients with refractory MCL displayed complete remission (CR) which was retrospectively predicted by molecular abnormalities highlighted in the initial biopsy. In a second part, a differential proteomic analysis was realized using SELDI-TOF technology in order to discover therapeutic targets in MCL, MZL and SLL. Tissue protein profiles of 58 fresh frozen biopsies (18 MCL, 20 MZL and 20 SLL) were acquired and then analysed by hierarchical clustering. Specific lymphoma proteomic signatures were identified based on the expression of 37 protein peaks. SELDI-assisted protein purification followed by LC-MS/MS allowed us to identify proteins overexpressed in both MCL and SLL tumors. Among them 2 histones, H2B and H4 were identified in MCL and SRP9 in SLL. We described therapeutic targets in B-cell NHL using focalized and global approaches. This targeting can lead to CR even in refractory NHL and are predictable in initial biopsies
Léonard, Guillaume. "Analyses rhéologiques des systèmes granulaires appliquées à l'étude des effets des forces électrostatiques." Thèse, Université de Sherbrooke, 2011. http://savoirs.usherbrooke.ca/handle/11143/1948.
Roussel, Olivier. "Les interfaces semiconductrices dans les cellules photovoltaïques à base de CuIn(S,Se)2." Paris 6, 2007. http://www.theses.fr/2007PA066717.
Claireaux, Mathieu. "Analyses phénotypique et fonctionnelle des cellules T CD4+ spécifiques du VIH chez les patients contrôlant spontanément l’infection à VIH." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCC264/document.
HIV Controllers are rare individuals able to spontaneously control viral replication in the absence of treatment. Several studies showed that controllers develop effective anti-viral T cell responses. Gag-specific CD4+ T cells could play a particular role in HIV control, because this population is preserved in comparison with the treated patients and correlates negatively with the viral load. In order to study this population, we performed a multiplexed single cell transcriptional and protein analysis from CD4+ T cells detected ex vivo by MHC-II tetramer labeling against the Gag293 peptide (Tet+). We compared the expression of 44 genes and 6 surface proteins in 9 Controllers patients and 9 treated patients. Firstly, we validated the high frequency of Tet+ CD4+ T cells in controllers compared to the treated patients, then we showed that Tet+ CD4+ T cells from controllers were activated and engaged in advanced Th1 differentiation with a cytotoxic profile. In addition, Tet+ CD4+ T cells from controllers showed a limited state of exhaustion, reflected by a lower expression of PD-1, which could be one of the reasons for maintaining their frequency and functions. In a second study, we studied follicular helper T cells (Tfh) among the Gag-specific CD4+ T cell population of HIV controllers. Tfh plays an essential role in the affinity maturation of the antibody response by providing help to B cells. To determine whether this CD4+ T cell subset may contribute to the spontaneous control of HIV infection, we analyzed the phenotype and function of circulating Tfh (cTfh: T cells CD4+ CD45RA- CXCR5+). We performed a MHC-II tetramer labeling against Gag293 peptide to detect HIV-specific cTfh (cTfh Tet +), and showed that this population is preferentially maintained in HIV controllers. Phenotypic analysis of Tet+ cTfh population showed a higher intensity of PD-1 expression (MFI) in the treated group suggesting abnormal immune activation in these patients. The function of cTfh, analyzed by the capacity to promote IgG secretion in cocultures with autologous memory B cells, did not show major differences between groups in terms of total IgG production. However, the production of HIV-specific IgG is significantly more efficient in the controller group, especially for the anti-Env response that is more than 30-fold greater than those of the treated patients. Finally, the frequency of Tet+ cTfh correlated positively with the production of specific IgG, supporting the idea of an important role of Tfh function in the humoral antiHIV response. Taken together, these results indicate that Gag-specific CD4+ T cell population supports the two arms of the antiviral immune response in HIV controllers: the cell-mediated response through a preferential differentiation toward Th1 cell type showing a cytotoxic profile, and the humoral response, reflected by preserved cTfh / B interactions, resulting in a vigorous memory response. Maintaining the function and frequency of these Gag-specific CD4+ T cells could therefore play an important role in HIV control
Ouedraogo, Marion. "Identification de gènes co-exprimés et co-localisés par des analyses multivariées : analyse des groupes de gènes co-exprimés en fonction des interactions physiques à l’échelle du génome." Rennes, Agrocampus Ouest, 2013. http://www.theses.fr/2013NSARB234.
Many analyses showed that the genome architecture and physical interactions between chromosomes play a major role in the regulation of gene expression. For example, , the chromosomes in eukaryotic genomes are arranged in chromosomal territories. At the interface of these territories, some physical interactions enhance or silence gene expression. Furthermore, genes are highly expressed in some hot spots in the nucleus called transcription factories. Recently, new methods of molecular biology revealed physical interactions among the genome. The main objective of this project was to bring new insight concerning the impact of genome organisation on the regulation of gene expression. To this aim, we have chosen a Bioinformatics approach based on the following hypothesis: as the genome organisation in the nucleus affects gene expression, gene expression could in some part reveal the genome organisation. We have developed a method based on multivariate analysis and called Co-expression and Co- location Mapping that identifies the groups of co-expressed and neighbouring (co-located) genes. The method requires expression data and genomic locations of the genes. It retrieves the list of groups of co-expressed and co-located genes and the relation of co-expression between the groups. We have compared the groups identified by CoCoMap with data of physical interaction within the genome. A large proportion of the groups was associated with physical interaction, consolidating our original hypothesis. CoCoMap is a new way to analyse expression data by taking into account the importance of the location of the genes among their expression
Gosselin, Pauline. "Analyses structurales et fonctionnelles des interactions entre elF4E et ses partenaires." Phd thesis, Paris 6, 2012. http://hal.upmc.fr/tel-00829452.
The control of mRNA translation is a complex process that is critical for gene expression during development and many physiological processes. During translation initiation in eukaryotes, the Initiation Factor 4E (eIF4E) binds the cap structure of the mRNA and recruits the large scaffolding protein eIF4G to form the initiation complex, step that is often the major site of protein synthesis control. Interaction between eIF4E and eIF4G is targeted by the small translational repressor 4E-BP and other specific eIF4E-interacting partners (4E-IPs), which share with eIF4G a similar eIF4E-binding motif and compete for eIF4E to modulate its functions at different levels. Commonly, the repressor 4E-BP is described as a completely disordered protein, even in its eIF4E-bound state. In the present work, we showed that 4E-BP adopts in fact a folded structure when it interacts with eIF4E, establishing fuzzy and dynamic contacts that involve a larger binding footprint of 4E-BP on eIF4E. These results brought new insight into the mechanisms involved in the interaction between eIF4E and its partners, and emphasized the role of structural studies to develop new therapies, particularly in cancer treatments. During my thesis, we also developed a new approach that combines structural, in silico and biochemical analyses to find novel 4E-IPs. Among the new putative 4E-IPs, we characterized Angel1, a protein related to a family of deadenylases. All together, these results have opened up new perspectives in term of mRNA metabolism and specific regulations that target eIF4E
Gosselin, Pauline. "Analyses structurales et fonctionnelles des interactions entre elF4E et ses partenaires." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2012. http://tel.archives-ouvertes.fr/tel-00829452.
Mascalchi, Patrice. "Analyse par suivi de particule unique à la surface de lymphocytes vivants de l'organisation dynamique des récepteurs CD4 et CCR5 impliqués dans l'infection par le VIH." Toulouse 3, 2012. http://thesesups.ups-tlse.fr/1560/.
Infection of CD4+ T lymphocytes by the human immunodeficiency virus (HIV) is initiated by the sequential interaction of the viral envelope protein gp120 with the primary receptor CD4 and then a coreceptor, CCR5 in most cases of primo-infection. The necessity of this double interaction suggests that the efficiency of the HIV entry process could depend on the dynamic membrane organization of these two receptors. To study this organization at the surface of living lymphocytes, we used single particle tracking (SPT), a high resolution and non-invasive microscopy approach. Firstly, we validated the choice of Quantum dots (QD) for SPT experiments based on the results of a systematic study that evaluated the influence of the particle on the measured diffusion coefficient. Secondly, we determined and analyzed the movement of CD4 and CCR5 receptors labeled with QD, at the surface of lymphocytes immobilized on glass coverslips. These experiments showed that both receptors exhibit three different diffusion modes: random, permanently or transiently confined diffusion. Addition of molecules that destabilize the CD4-CCR5 interaction (soluble CD4, maraviroc) revealed that it is partially responsible for their confinement. All these observations allow us to establish the basis for a model of the dynamic membrane organization of CD4 and CCR5 at the surface of living lymphocytes. These data represent a starting-point for the understanding of the presumed relationship between the dynamic organization of the receptors and the first steps of the HIV infection process
Bachy, Charles. "Phylogénie, diversité et dynamique temporelle chez les ciliés tintinnidés marins." Phd thesis, Université Paris Sud - Paris XI, 2012. http://tel.archives-ouvertes.fr/tel-00769949.
Sapay, Nicolas. "Les peptides d'ancrage à l'interface membranaire : analyses structurales par RMN et dynamique moléculaire et développement d'une méthode de prédiction bioinformatique." Lyon 1, 2006. http://www.theses.fr/2006LYO10003.
Colin, Camille. "Développement de nouvelles méthodes de microscopie et d’électrochimie pour des analyses multi-paramétriques de mitochondries individuelles cardiaques." Thesis, Bordeaux, 2020. http://www.theses.fr/2020BORD0149.
The importance of mitochondria in the regulation of cellular metabolism, from physiological (cardiac contraction, etc.) or pathological (cancer, Alzheimer's, etc.) processus are well established. In the context of heart contraction, which is a highly ATP-dependent process, the exact intervention of the mitochondrion remains a subject of debate today. One hypothesis suggests that the mitochondria see only a small percentage (1%) of the calcium flow necessary for contraction, while another hypothesis suggests that the mitochondria, which produce 90% of cellular ATP, are activated by this calcium flow at each contraction to supply energy demand. Part of the answer may be in the opening of the mitochondrial permeability transition pore (mPTP), which is mainly activated by calcium. If this non-specific pore is well described for its pathological opening, notably in ischemia-reperfusion by triggering apoptosis, this is its physiological opening mode which would be important in the cardiac context by playing a crucial role in the control of mitochondrial calcium flows. However, this mode of opening is still weakly characterized, in particular because the techniques used are often based on the average monitoring of large mitochondrial populations. However, more and more studies show the existence of mitochondrial subpopulations within a cell, with differences in activities between them. The objective of this study was to develop new methods of analysis, in order to be able to follow the variations of activities of the populations but especially, to be able to analyze individual mitochondria. By Based on these methods, we could study the patho-physiological openings of mPTP in the context of heart contraction was conducted.The first approach that I developed is based on optical microscopy, it consists of three main steps: 1) processing of microscopy images, 2) identification of mitochondria and their monitoring them over time, 3) data analyses. The second approach was based on electrochemistry, we performed a simultaneous detection of mitochondrial oxygen consumption and the reduction rate of quinones of the respiratory chain. To characterize these methods, we first followed the classical mitochondrial bioenergetic states. We have thus shown a wide variety of responses with the observation of two mitochondrial subpopulations of distinct sizes. Then, in a second step, we used fluorescence microscopy to follow, at the single mitochondrion level, transient variations in the membrane potential that we connect to the openings of the mPTP. We have thus confirmed that the activation of the pathological opening mode can be induced by a calcium concentration transient, and is inhibited by cyclosporin A (CsA). Strikingly, we observed transient openings of mPTP, activated also by calcium and by photo-illumination as well, however in our study this mode of opening is not inhibited by CsA which suggests a different mechanism
Carabana, Garcia Claudia. "Defining cell fate specification of mouse Mammary Stem Cells in 4D." Electronic Thesis or Diss., Université Paris sciences et lettres, 2022. http://www.theses.fr/2022UPSLS055.
DEFINING CELL FATE SPECIFICATION OF MOUSE MAMMARY STEM CELLS IN 4DCoordination of cell fate specification and branching morphogenesis is necessary to generate an organ with its specialized final structure and function. Accordingly, how different cell types are specified in a tightly regulated manner in time and space, in order to drive the morphogenesis of a complex tissue, remains a major question in the field of developmental biology.The mammary gland (MG) consists in a branched bi-layered epithelium composed of an outer layer of basal cells (BCs) and an inner compartment of polarised luminal cells (LCs). In this tissue, adult homeostasis is exclusively maintained by lineage-restricted unipotent progenitors, whereas multipotent mammary stem cells (MaSCs) are only found in the embryonic gland, making it an ideal tissue paradigm to study stem cell dynamics and lineage specification, as well as their contribution to tissue morphogenesis.WORKING HYPOTHESISOur recent results showed that multipotent MaSCs become lineage-restricted around embryonic day E15.5, coinciding with the first morphogenetic events that establish the mammary ductal network. We thus hypothesized that loss of multipotency in the mammary gland was linked to cell rearrangements, leading to the branching of embryonic mammary buds. However, the exact timing and the mechanisms responsible for the switch from multipotency to unipotency during embryonic MG are still unknown.AIM AND METHODOLOGYThe overarching aim of this project was to characterise the stem cell dynamics underlying MaSCs differentiation during MG development, and to define the transcriptional signals underpinning this process. We have approached this ambitious objective combining two approaches: 1) single-cell RNA sequencing analysis at different embryonic times, to discover which signals determine cell identity during mammary development, and 2) a live lineage tracing approach in ex vivo embryonic mammary cultures to study dynamic cell behaviours and rearrangements during the earliest phases of mammary growth.RESULTSWe found that lineage restriction is a progressive developmental process. By single cell transcriptomics, we identified a single population of mammary epithelial cells at E13.5, but we could distinguish three transcriptionally distinct cell subsets at E15.5, which included luminal-like, basal-like and hybrid cells co-expressing luminal and basal genes. Spatial transcriptomic analysis revealed that the basal-like and luminal-like clusters were indeed already spatially restricted in the embryonic mammary bud, being positioned either in close proximity to the basement membrane or in the inner bud region, respectively. Importantly, this analysis revealed novel molecular markers of committing LCs and BCs, that cannot be distinguished with known adult MG markers.Additionally, we report the transcriptional signatures distinguishing two spatially restricted embryonic mammary mesenchymal cell populations, representing sub-epithelial and dermal mesenchyme. Long-term live-imaging revealed that paracrine signalling from embryonic mesenchyme to epithelial cells, via Fgf10-Fgfr2, influences epithelial branching.We then developed a deep learning-based pipeline to semi-automatically track individual cells and tissue branches in embryonic mammary explants analysed by time-lapse microscopy. We show that the initial steps of morphogenesis are characterized by highly dynamic cell rearrangements in the growing branch tips. However, forced activation of the Wnt/b-catenin pathway in the embryonic mammary epithelium precluded branching in vivo and ex vivo, indicating that epithelial Wnt signalling is an essential regulator of mammary branching morphogenesis.This work sheds light on the timing and mechanisms governing mammary cell fate decisions, providing potential biomarkers of breast cancer, which often arises from reactivation of embryonic multipotency programs
Aupérin, Anne. "Carcinomes broncho-pulmonaires non à petites cellules localement avancées : évaluation de la chimiothérapie associée à la radiothérapie par les méta-analyses sur données individuelles." Paris 11, 2010. http://www.theses.fr/2010PA11T017.