Academic literature on the topic 'Multiomique'
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Dissertations / Theses on the topic "Multiomique"
Claude, Olivier. "Identification de marqueurs membranaires spécifiques de cellules progénitrices cardiaques PW1+ par une approche multiomique." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS116.
Full textIschemic heart diseases are the major cause of heart faillure, one of the most concerning disease in the world. The scarring process following myocardial infarction has been shown to be driven by cardiac progenitors celles (CPC), and PW1+ CPCs were shown to mediate and participate to this process. To target PW1+ cells, we are limited to a PW1nLacZ reporter mice model. We aim to find a membrane bound protein associated with PW1 presence to help to target specifically those cells. Using a prediction software suite, we predicted a specific membranome for PW1+ CPCs from RNA-Seq datas. We performed a mass spectrometry analysis to determine an observed membranome, and the combination of both approaches allowed us to find candidates to test. We then confirmed the expression of the candidates, and one showed strong sensibility and sensibility to describe PW1+ cells. The inhibition of this target by pharmacological drug in vitro and in vivo showed a significant decrease of fibrosis in a myocardial infarction murine model together with a significant increase of survival after treatment
Proust, Lucas. "Analyse multiomique des peptides d’extraits de levure et de leurs impacts fonctionnels sur Streptococcus thermophilus." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLA032.
Full textLactic acid bacteria are widely used as starters in dairy industry. They are generally produced in complex fermentation media containing a wide array of nutrients that can be provided by yeast extracts (YEs). The main goal of this thesis project, involving two industrial partners, Lesaffre and Sacco, as well as INRA, was to investigate the effect of the peptide fraction of two YEs (YE1 and YE2) on an industrial Streptococcus thermophilus strain, a major lactic acid starter. The underlying hypothesis of this whole project was that YE peptides could have a role in nutrition but also regulate cellular functions of technological relevance. In order to explore this question, a two-step strategy was elaborated: i) mass spectrometry characterization (peptidomics) of both YE peptide fractions and time course analysis of their relative abundance during the growth in bioreactors of S. thermophilus, and ii) parallel time course analysis of the strain transcriptome and proteome. The final objective was to cross these two levels of information in order to correlate differences of peptide content with differentially activated systems related to technological performances.YE peptidome characterization and kinetic analysis first required an important methodological development. It eventually resulted in a complete analytical tool that combines high throughput peptidomic analysis as well as bioinformatic and statistical data processing. This powerful tool was able to identify around 4,000 different peptides in both YEs. Then, the time course analysis also clarified the in vivo substrate specificities of the oligopeptide transport system of the bacterium (Ami). A peptide positive net charge notably turned out to be the leading factor governing peptide transport. In addition to this semi-quantitative approach, quantitative analyses were carried out on YE peptide fractions (differential HPLC analyses of amino acids before and after sample hydrolysis). They notably revealed significant differences in oligopeptides content between both YEs.Meanwhile, genome scale transcriptomic and proteomic analyses performed during the strain growth highlighted two significant events. The first one concerns the overexpression in YE1 of a quorum sensing-based genetic locus that uses a pheromone peptide as molecular signal. The second event relates to several biosynthesis pathways (amino acids and purines) that were differentially affected by both YEs. These dynamics could result from differences in peptide content between both substrates. In particular, some pathways could have been differentially modulated by central regulators such as CodY, whose activity is correlated to the medium peptide richness, or YebC, a CodY-like regulator whose functional link with CodY is still unknown in S. thermophilus. All these results open avenues for a better understanding of the interplay between peptides and bacterial metabolism. In the future, this whole approach could lead to the identification of performance biomarkers in YEs, which in turns may eventually translate into the conception of new customized products granting high technological performances to dairy starters
Moutard, Laura. "Οptimisatiοn de la spermatοgenèse in vitrο chez la sοuris prépubère : rôle majeur des cellules sοmatiques testiculaires et de la stérοïdοgenèse." Electronic Thesis or Diss., Normandie, 2024. http://www.theses.fr/2024NORMR019.
Full textTreating children for adverse effects related to cancer treatment is a major public health issue. As cancer treatments are known to have a toxic effect on the gonads, fertility preservation procedures are being introduced. In prepubertal boys, testicular tissue sampling followed by freezing is suggested. After thawing, testicular tissue can be matured in vitro or in vivo to produce sperm for assisted reproduction. In vitro maturation could be proposed to patients with testicular localization of residual tumor cells. However, in vitro sperm production remains a rare event in the mouse model. This protocol cannot therefore be transposed to the clinic at present. Our first study shows partial maturation of Leydig cells, disturbed steroidogenic activity, and excess estrogen in in vitro matured tissue, while the second demonstrates maturation of Sertoli cells in vitro. A better understanding of the molecular mechanisms within cultured tissues was needed to adapt the culture medium and optimize spermatogenesis yields in vitro. We therefore used a new multiomics approach combining single nuclei RNA-seq and single nuclei ATAC-seq to simultaneously profile gene expression and open chromatin in the same cell. Before any clinical application can be envisaged, it is essential to continue this work by optimizing the various stages of spermatogenesis, separately mitosis, meiosis and spermiogenesis, by determining which factors are essential during these stages, to develop a sequential culture protocol
Richerd, Mathilde. "Développement d'un système de microfluidique de gouttes pour l'analyse d'échantillons complexes." Thesis, Université Paris sciences et lettres, 2021. http://www.theses.fr/2021UPSLS051.
Full textDroplet microfluidics is a technology with a huge potential for miniaturization and automation of conventional methods in bioanalysis. Indeed, droplet microfluidics has many functionalities, such as merging, sorting and cell encapsulation, that can reproduce manipulations in standard protocols in bioanalysis on very small volumes with advantages such as a low samples and reagents consumption and reduction of analysis duration. During this thesis, we developed protocols for two types of biological analysis, using magnetic particles manipulation in 100 nL droplets.The first project is about single cell multiomics analysis. We implemented a droplet microfluidics protocol for the separation of mRNA and DNA from complex samples: from a mix of pre-purified RNA and DNA to a suspension of less than ten cells. At each steps, the droplet system performances were evaluated and the results were compared to extractions made in tubes in a non-microfluidics way. The results are very promising since they demonstrate for the first time in such a system the sequential separation of DNA and RNA from cell lysate or a few cells encapsulated and lysed in droplets.The second project is about the sample preparation in droplet for MALDI-TOF mass spectrometry analysis. This project was built in collaboration researchers from CEA Saclay. They have shown that it is very interesting to deposit samples in droplets on MALDI plates to increase the detection sensitivity thanks to a focusing effect. We have implemented on an original integrated droplet microfluidic approach for protein analysis by MALDI-TOF MS: from in drop sample preparation by supported enzymatic digestion to on plate deposition and peptides local pre-concentration. Development was done with lysozyme as a model protein and thanks to our in-drop digestion and deposition protocol we identified this protein by mass fingerprint from 200 fmol protein with a good reliability
Nicoud, Quentin. "Study of terminal bacteroid differentiation features during the legume-rhizobium symbiosis Bradyrhizobium diazoefficiens USDA110 nodulation of Aeschynomene afraspera is associated with atypical terminal bacteroid differentiation and suboptimal symbiotic efficiency Sinorhizobium meliloti functions required for resistance to the antimicrobial NCR peptides and bacteroid differentiation." Thesis, université Paris-Saclay, 2021. http://www.theses.fr/2021UPASB007.
Full textThe legume-rhizobia symbiosis is a close interaction between a plant and bacteria. During this symbiosis, bacteria are hosted by the plants in symbiotic organs called nodules and in which the symbionts fix atmospheric nitrogen for the plants. Legume species from IRLC and Dalbergioid can control symbiotic rhizobia and mediate a particular differentiation process through the massive production of nodule-specific cysteine-rich (NCR) peptides. In vitro, cationic NCR peptides have membrane-permeabilizing activities on many bacteria. How rhizobia adapt to resist this intense stress remains poorly understood. Two main research axes were driven during this thesis, both linked to the understanding of how bacteria react to terminal differentiation imposed by NCR peptides. On one side, we tried to functionally analyze bacterial functions for their role in NCR resistance during the model interaction between Medicago truncatula and Sinorhizobium meliloti. In this work, we mainly assessed membrane functions such as LPS synthesis, Envelope Stress Response, and import functions. We found novel functions that could be involved in NCR resistance and terminal bacteroid differentiation.On the other side, we conducted a multi-omics approach coupled with cell-biology techniques to characterize the ill-adapted interaction between Bradyrhizobium diazoefficiens USDA110 and Aeschynomene afraspera. We discovered new features in this interaction with an unusual differentiation
Denecker, Thomas. "Bioinformatique et analyse de données multiomiques : principes et applications chez les levures pathogènes Candida glabrata et Candida albicans Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite FAIR_Bioinfo: a turnkey training course and protocol for reproducible computational biology Label-free quantitative proteomics in Candida yeast species: technical and biological replicates to assess data reproducibility Rendre ses projets R plus accessibles grâce à Shiny Pixel: a content management platform for quantitative omics data Empowering the detection of ChIP-seq "basic peaks" (bPeaks) in small eukaryotic genomes with a web user-interactive interface A hypothesis-driven approach identifies CDK4 and CDK6 inhibitors as candidate drugs for treatments of adrenocortical carcinomas Characterization of the replication timing program of 6 human model cell lines." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL010.
Full textBiological research is changing. First, studies are often based on quantitative experimental approaches. The analysis and the interpretation of the obtained results thus need computer science and statistics. Also, together with studies focused on isolated biological objects, high throughput experimental technologies allow to capture the functioning of biological systems (identification of components as well as the interactions between them). Very large amounts of data are also available in public databases, freely reusable to solve new open questions. Finally, the data in biological research are heterogeneous (digital data, texts, images, biological sequences, etc.) and stored on multiple supports (paper or digital). Thus, "data analysis" has gradually emerged as a key research issue, and in only ten years, the field of "Bioinformatics" has been significantly changed. Having a large amount of data to answer a biological question is often not the main challenge. The real challenge is the ability of researchers to convert the data into information and then into knowledge. In this context, several biological research projects were addressed in this thesis. The first concerns the study of iron homeostasis in the pathogenic yeast Candida glabrata. The second concerns the systematic investigation of post-translational modifications of proteins in the pathogenic yeast Candida albicans. In these two projects, omics data were used: transcriptomics and proteomics. Appropriate bioinformatics and analysis tools were developed, leading to the emergence of new research hypotheses. Particular and constant attention has also been paid to the question of data reproducibility and sharing of results with the scientific community
Book chapters on the topic "Multiomique"
LÉVY-LEDUC, Céline, Marie PERROT-DOCKÈS, Gwendal CUEFF, and Loïc RAJJOU. "Sélection de variables dans le modèle linéaire général : application à des approches multiomiques pour étudier la qualité des graines." In Intégration de données biologiques, 101–28. ISTE Group, 2022. http://dx.doi.org/10.51926/iste.9030.ch4.
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