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. mPies’ 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 géographie protohistorique en contexte de moyenne montagne : enquête en Haute-Auvergne et sur les plateaux limousins (Massif central, France)

Le nord-ouest du Massif central est un terrain privilégié pour étudier l’occupation au cours de la Protohistoire dans un contexte de moyenne montagne. Au cours d’un doctorat, plusieurs sites de hauteur de Haute-Auvergne (Cantal, Auvergne-Rhône-Alpes) et de haute Corrèze (Nouvelle-Aquitaine) ont fait l’objet de prospections, de sondages et d’études de mobilier. Pour l’âge du Bronze et le premier âge du Fer, des données inédites permettent de reconsidérer les modalités d’occupation de ces territoires. À l’aide d’analyses spatiales, les rythmes d’occupation de ces sites et leurs caractéristiques d’implantation ont été examinés. Des esquisses de dynamique d’occupation peuvent être proposées, en particulier entre le Bronze moyen et La Tène ancienne. Ainsi, la disposition des sites de hauteur n’apparaît pas comme anodine : elle s’appuie sur des voies de passages naturelles, plus ou moins utilisées au cours du temps, et un maillage régulier du territoire se dessine à certaines périodes.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-Rhône-Alpes) and of Haute-Corrèze (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 doesn’t 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 phenotype–genotype 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 DNA–protein 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 DNA–protein 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