Search results for "RNA seq"
showing 9 items of 39 documents
Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient
2021
Synchronous primary malignancies occur in a small proportion of head and neck squamous cell carcinoma (HNSCC) patients. Here, we analysed three synchronous primaries and a recurrence from one patient by comparing the genomic and transcriptomic profiles among the tumour samples and determining the recurrence origin. We found remarkable levels of heterogeneity among the primary tumours, and through the patterns of shared mutations, we traced the origin of the recurrence. Interestingly, the patient carried germline variants that might have predisposed him to carcinogenesis, together with a history of alcohol and tobacco consumption. The mutational signature analysis confirmed the impact of alc…
Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Primin…
2022
Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial…
Evolved high aerobic capacity has context-specific effects on gut microbiota
2022
Publisher Copyright: Copyright © 2022 Hanhimäki, Watts, Koskela, Koteja, Mappes and Hämäläinen. Gut microbiota is expected to coevolve with the host's physiology and may play a role in adjusting the host's energy metabolism to suit the host's environment. To evaluate the effects of both evolved host metabolism and the environmental context in shaping the gut microbiota, we used a unique combination of (1) experimental evolution to create selection lines for a fast metabolism and (2) a laboratory-to-field translocation study. Mature bank voles Myodes glareolus from lines selected for high aerobic capacity (A lines) and from unselected control (C lines) were released into large (0.2 ha) outdo…
Evolution of common ragweed (Ambrosia artemisiifolia) resistance to herbicides : identification of genetic determinisms and application to molecular …
2022
Common ragweed (Ambrosia artemisiifolia L.), a particularly troublesome and allergenic weed, is mainly controlled in agricultural fields using ALS inhibitor herbicides. Recent cases of herbicide resistance have been reported in France and are jeopardising the efficacy of this mode of action. Both target site resistance (TSR, structural mutation in ALS gene) and non target site resistance (NTSR, regulatory and/or structural mutations in secondary metabolism) are involved. The fundamental aim of this work was to identify the genetic determinisms of resistance to ALS inhibitors that have evolved in common ragweed populations in France. As an applied objective, this work also aimed to prepare t…
Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage fr…
2015
The diversity of lactic acid bacteria (LAB) associated with chicha, a traditional maize-based fermented alcoholicbeverage from Northwestern Argentina, was analyzed using culture-dependent and culture-independent approaches.Samples corresponding to 10 production steps were obtained from two local producers at Maimará(chicha M) and Tumbaya (chicha T). Whereas by culture-dependent approach a few number of species(Lactobacillus plantarum and Weissella viridescens in chicha M, and Enterococcus faecium and Leuconostocmesenteroides in chicha T) were identified, a higher quantitative distribution of taxa was found in both beveragesby pyrosequencing. The relative abundance of OTUs was higher in chic…
Natural soil reservoirs for human pathogenic and fecal indicator bacteria
2015
Prod ? EA UB INRA BIOME; International audience; résumé du livre : Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manuall is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradati…
Evolution of herbicide resistance in mugwort (Ambrosia artemisiifolia L.): search for genetic determinisms and application to molecular diagnosis
2022
Common ragweed (Ambrosia artemisiifolia L.), a particularly troublesome and allergenic weed, is mainly controlled in agricultural fields using ALS inhibitor herbicides. Recent cases of herbicide resistance have been reported in France and are jeopardising the efficacy of this mode of action. Both target site resistance (TSR, structural mutation in ALS gene) and non target site resistance (NTSR, regulatory and/or structural mutations in secondary metabolism) are involved. The fundamental aim of this work was to identify the genetic determinisms of resistance to ALS inhibitors that have evolved in common ragweed populations in France. As an applied objective, this work also aimed to prepare t…
Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. Original strategies against emerging viruses
2021
Guanine quadruplexes (G4) structures in viral genome have a key role in modulating viruses’ biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modelling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.
Exercise-Induced Extracellular Vesicles Delay the Progression of Prostate Cancer
2022
Increasing evidence suggests that regular physical exercise not only reduces the risk of cancer but also improves functional capacity, treatment efficacy and disease outcome in cancer patients. At least partially, these effects are mediated by the secretome of the tissues responding to exercise. The secreted molecules can be released in a carrier-free form or enclosed into extracellular vesicles (EVs). Several recent studies have shown that EVs are actively released into circulation during physical exercise. Here, we for the first time investigated the effects of exercise-induced EVs on the progression of cancer in an F344 rat model of metastatic prostate cancer. Although we did not observe…