292 research outputs found
mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPiesâ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/
Essai de gĂ©ographie protohistorique en contexte de moyenne montagne : enquĂȘte en Haute-Auvergne et sur les plateaux limousins (Massif central, France)
Le nord-ouest du Massif central est un terrain privilĂ©giĂ© pour Ă©tudier lâoccupation au cours de la Protohistoire dans un contexte de moyenne montagne. Au cours dâun doctorat, plusieurs sites de hauteur de Haute-Auvergne (Cantal, Auvergne-RhĂŽne-Alpes) et de haute CorrĂšze (Nouvelle-Aquitaine) ont fait lâobjet de prospections, de sondages et dâĂ©tudes de mobilier. Pour lâĂąge du Bronze et le premier Ăąge du Fer, des donnĂ©es inĂ©dites permettent de reconsidĂ©rer les modalitĂ©s dâoccupation de ces territoires. Ă lâaide dâanalyses spatiales, les rythmes dâoccupation de ces sites et leurs caractĂ©ristiques dâimplantation ont Ă©tĂ© examinĂ©s. Des esquisses de dynamique dâoccupation peuvent ĂȘtre proposĂ©es, en particulier entre le Bronze moyen et La TĂšne ancienne. Ainsi, la disposition des sites de hauteur nâapparaĂźt pas comme anodine : elle sâappuie sur des voies de passages naturelles, plus ou moins utilisĂ©es au cours du temps, et un maillage rĂ©gulier du territoire se dessine Ă certaines pĂ©riodes.The Northwestern area of Massif Central is a privileged ground for the study of Protohistoric human occupation in a mid-mountain context. For the purpose of a PhD, many entrenched or hilltop settlements of Haute-Auvergne (Cantal, Auvergne-RhĂŽne-Alpes) and of Haute-CorrĂšze (Nouvelle-Aquitaine) have been subjected to prospections, surveys, or studies of collections. For Bronze Age and Early Iron Age, new data are now available, and allow us to reconsider the occupation modalities of these territories. With spatial analyses, the occupation rhythms of these sites and their characteristics can be observed and discussed. The first drafts of occupation dynamics in western Massif Central during Protohistory can be proposed, especially between the Middle Bronze age and La Tene I for the Haute-Auvergne. Thus, the positioning of hilltop settlements doesnât appear as random: it is based on more-or-less used in time natural passage ways, and designs a regular territorial network in certain periods
Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotypeâgenotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study
Detection of single DNA molecules by multicolor quantum-dot end-labeling
Observation of DNAâprotein interactions by single molecule fluorescence microscopy is usually performed by using fluorescent DNA binding agents. However, such dyes have been shown to induce cleavage of the DNA molecule and perturb its interactions with proteins. A new method for the detection of surface-attached DNA molecules by fluorescence microscopy is introduced in this paper. Biotin- and/or digoxigenin-modified DNA fragments are covalently linked at both extremities of a DNA molecule via sequence-specific hybridization and ligation. After the modified DNA molecules have been stretched on a glass surface, their ends are visualized by multicolor fluorescence microscopy using conjugated quantum dots (QD). We demonstrate that under carefully selected conditions, the position and orientation of individual DNA molecules can be inferred with good efficiency from the QD fluorescence signals alone. This is achieved by selecting QD pairs that have the distance and direction expected for the combed DNA molecules. Direct observation of single DNA molecules in the absence of DNA staining agent opens new possibilities in the fundamental study of DNAâprotein interactions. This work also documents new possibilities regarding the use of QD for nucleic acid detection and analysis
Literacy in Finland. Country Report. Children and adolescents
European Literacy Policy Network (ELINET
Literacy in Scotland. Country Report. Children and adolescents
European Literacy Policy Network (ELINET
- âŠ