Academic literature on the topic 'Séquençage Nanopore'
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Journal articles on the topic "Séquençage Nanopore"
Montel, Fabien. "Séquençage de l’ADN par nanopores." médecine/sciences 34, no. 2 (February 2018): 161–65. http://dx.doi.org/10.1051/medsci/20183402014.
Full textChikhaoui, Lies. "Étude du transcriptome circadian chez la souris à l’aide de séquençage long read Oxford Nanopore." Médecine du Sommeil 18, no. 4 (December 2021): 192. http://dx.doi.org/10.1016/j.msom.2021.10.019.
Full textAudebert, Christophe, David Hot, and Ségolène Caboche. "Séquençage par nanopores." médecine/sciences 34, no. 4 (April 2018): 319–25. http://dx.doi.org/10.1051/medsci/20183404012.
Full textJordan, Bertrand. "Séquençage d’ADN : l’offensive des nanopores." médecine/sciences 33, no. 8-9 (August 2017): 801–4. http://dx.doi.org/10.1051/medsci/20173308028.
Full textDissertations / Theses on the topic "Séquençage Nanopore"
Theulot, Bertrand. "Étude de la dynamique de réplication du génome de Saccharomyces cerevisiae par séquençage nanopore." Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS565.
Full textIn eukaryotes, DNA replication initiates from multiple origins activated throughout S-phase. Each origin forms two diverging replication forks that synthesize DNA. Although genome duplication depends on a proper fork progression, the governing factors are poorly understood, and little is known about replication fork velocity variations along eukaryotic genomes. My thesis project aimed at generating in the budding yeast S. cerevisiae the first ever genome-wide map of fork progression based on individual fork rates. Our laboratory has recently introduced a high-throughput, high-resolution, single molecule-based replication mapping technique relying on the detection by nanopore sequencing of 5-bromo-2’-deoxyuridine (BrdU), a thymidine analogue incorporated in replicating DNA. In collaboration with bioinformaticians, I have developed NanoForkSpeed (NFS), a method capable of positioning, orienting and extracting the velocity of replication forks from BrdU tracks synthesized during a brief pulse-labelling of asynchronously growing cells. In addition, I have engineered the BT1 yeast strain which exhibits highly efficient BrdU incorporation and wild-type growth, allowing the measurement of fork progression in physiologically relevant conditions. NFS retrieves previous S. cerevisiae mean fork speed estimates (≈2 kb/min) and precisely quantifies speed changes in cells with altered replisome progression or exposed to hydroxyurea. The positioning of >125,000 fork velocities provides a genome-wide map of fork progression based on individual fork rates, showing a uniform fork speed across yeast chromosomes except for a marked slowdown at known pausing sites, namely centromeres, telomeres, the ribosomal DNA and some tRNA genes. During my PhD, I have also created Nanotiming, a novel method to study the replication timing (RT) of S. cerevisiae's genome. Nanotiming relies on the quantification of BrdU rates in nanopore reads: since thymidine concentration increases during S-phase in yeast, BrdU incorporation will be lower in late replicating than in early replicating regions. In contrast to reference techniques based on DNA copy number analysis, which are either low-resolution or difficult to implement as they require cell synchronization or sorting, Nanotiming only demands the labeling of asynchronously growing yeast cells with BrdU during one doubling. RT profiles obtained both in wild-type cells and in a mutant strain where Rif1, a key RT regulator, has been inactivated are remarkably similar to those established by high-resolution methods, validating my approach. In addition to its simplicity, Nanotiming also paves the way for high-throughput analysis of single molecule RT and in-depth study of inter-individual RT variability
Sall, Salimata Ousmane. "Rôle des voies de signalisation des dommages à l'ADN dans le contrôle de l'architecture du génome et du méthylome en réponse aux stress génotoxiques chez Arabidopsis thaliana." Electronic Thesis or Diss., Strasbourg, 2023. http://www.theses.fr/2023STRAJ134.
Full textPlants, sessile organisms, are constantly exposed to various environmental factors and therefore need to develop sophisticated molecular mechanisms to ensure their survival and adaptation. Genotoxic stresses can lead to chromosomal rearrangements and changes in the epigenome, impacting transcriptional and developmental programs. It is thus important to study the relationship between genome and epigenome dynamics in response to genotoxic stress. In this thesis project, Arabidopsis thaliana was used as a model plant to study genome structure and methylome profile under ionizing (proton) and non-ionizing (UVB and UVC) genotoxic stress conditions. The role of two protein kinases (Ataxia telangiectasia mutated or ATM and Ataxia telangiectasia mutated RAD3-related or ATR), involved in DDR (DNA damage Repair), have been studied in genome integrity and methylome maintenance. Using an ONT (Oxford Nanopore Technology) sequencing approach, we revealed that genotoxic stress leads to structural variations (SV) consisting mainly in deletions and insertions, located in heterochromatin regions rich in transposable elements (TE) and intergenic regions (RI). We demonstrated that ATM and ATR protect the genome against SV at the vegetative stage and in response to genotoxic stress. In fact, TEs and genes are the main genetic entities targeted by ATM for their protection against SV, under stress conditions. We have determined that c-NHEJ (classical Non-Homologous End-Joining) is the predominant pathway for DSB repair compared to MMEJ (Microhomology-mediated end joining) and that ATM/ATR prevent the use of long MH (Microhomology) sequences leading to long deletions during MMEJ repair. DNA methylation profiles were determined by Bisulfite sequencing and/or ONT. We were able to identify changes in DNA methylation levels mainly at the TE level, in the CHH context in response to genotoxic stresses. We also demonstrated the involvement of ATR and especially ATM in the maintenance of methylome integrity at the gene and TE levels in the CG and CHH contexts respectively
Barrios, pérez María. "Design and computer simulations of 2D MeX2 solid-state nanopores for DNA and protein detection analysis." Thesis, Bourgogne Franche-Comté, 2020. http://www.theses.fr/2020UBFCK003.
Full textSolid-state nanopores (SSN) have emerged as versatile devices for biomolecule analysis. One of the most promising applications of SSN is DNA and protein sequencing, at a low cost and faster than the current standard methods. SSN sequencing is based on the measurement of ionic current variations when a biomolecule embedded in electrolyte is driven through a nanopore under an applied electric potential. As a biomolecule translocates through the nanopore, it occupies the pore volume and blocks the passage of ions. Hence, ultrafast monitoring of ionic flow during the passage of a biomolecule yields information about its structure and chemical properties. The size of the sensing region in SSN is determined by the size and thickness of the pore membrane. Therefore, two-dimensional (2D) transition metal dichalcogenides such as molybdenum disulfide (MoS2) arise as great candidates for SSN applications as an alternative to graphene. In the present work, we investigated the feasibility of using MoS2 nanopores for protein sequencing from all-atom molecular dynamics (MD) simulations. First, we studied the ionic conductance of MoS2 nanoporous membranes by characterizing the KCl electrolyte conductivity through MoS2 nanopores with diameters ranging from 1.0 to 5.0 nm and membranes from single to five-layers. Using MD simulations, we showed the failure of the usual macroscopic model of conductance for the nanoporous membranes with the smallest diameters and developed a modified model which proves usefulness to interpret experimental data. Second, we investigated the threading and translocation of individual lysine residues and a model protein with poly-lysine tags through MoS2 nanopores under the application of an electric potential. A proof-of principle technique based on the use of positively or negatively charged amino acids for protein translocation was proposed to promote the entrance of proteins through SSN in experiments. By analyzing the current-voltage curves simulated, we established the relationship between the translocation sequence events through the nanopores observed at the atomic scale in MD simulations, and the computed current fluctuations. Finally, experimental evidence of ionic conductance measurements in sub-nanometer (sub-nm) pores made of atomic defects has been recently reported. To give a better insight of the ionic transport through atomic scale pores, we performed MD simulations of sub-nm defect MoS2 pores using the reactive potential ReaxFF. Here, we characterized the variations of the atomic structure of the pores in vacuum and then we investigated the ionic conductance performance of one of the MoS2 defect pore membranes. ReaxFF potential was also useful to investigate the possible reactivity of MoS2 defect pore membranes with ethanol molecules. In addition, these simulations might provide a better understanding of the experimental setup of DNA sequencing, in which ethanol plays an unknown role in the sample preparation of the SSN