Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

2020 ◽  
Author(s):  
Alex Graudenzi ◽  
Davide Maspero ◽  
Fabrizio Angaroni ◽  
Rocco Piazza ◽  
Daniele Ramazzotti
Keyword(s):  
Large Scale ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Nucleotide Substitutions ◽  
Mutational Signatures ◽  
Mutational Hotspots ◽  
Scale Characterization ◽  
Definition Of ◽  
Mutational Processes

AbstractTo dissect the mechanisms underlying the inflation of variants in the SARS-CoV-2 genome, we present one of the largest up-to-date analyses of intra-host genomic diversity, which reveals that most samples present heterogeneous genomic architectures, due to the interplay between host-related mutational processes and transmission dynamics.The deconvolution of the set of intra-host minor variants unveils the existence of non overlapping mutational signatures related to specific nucleotide substitutions, which prove that distinct hosts respond differently to SARS-CoV-2 infections, and which are likely ruled by APOBEC, Reactive Oxygen Species (ROS) and ADAR.Thanks to a corrected-for-signatures dN/dS analysis we demonstrate that the mutational processes underlying such signatures are affected by purifying selection, with important exceptions. In fact, several mutations linked to low-rate mutational processes appear to transit to clonality in the population, eventually leading to the definition of new clonal genotypes and to a statistically significant increase of overall genomic diversity.Importantly, the analysis of the phylogenetic model shows the presence of multiple homoplasies, due to mutational hotspots, phantom mutations or positive selection, and supports the hypothesis of transmission of minor variants during infections. Overall, the results of this study pave the way for the integrated characterization of intra-host genomic diversity and clinical outcome of SARS-CoV-2 hosts.

scholarly journals Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

iScience ◽  
2021 ◽  
Vol 24 (2) ◽  
pp. 102116 ◽  
Author(s):  
Alex Graudenzi ◽  
Davide Maspero ◽  
Fabrizio Angaroni ◽  
Rocco Piazza ◽  
Daniele Ramazzotti
Keyword(s):  
Host Response ◽  
Large Scale ◽  
Genomic Diversity ◽  
Mutational Signatures ◽  
Scale Characterization

scholarly journals Remote Sensing Methods for the Biophysical Characterization of Protected Areas Globally: Challenges and Opportunities

2021 ◽  
Vol 10 (6) ◽  
pp. 384
Author(s):  
Javier Martínez-López ◽  
Bastian Bertzky ◽  
Simon Willcock ◽  
Marine Robuchon ◽  
María Almagro ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Protected Areas ◽  
Large Scale ◽  
Anthropogenic Activities ◽  
Global Scale ◽  
Area Network ◽  
Biophysical Characterization ◽  
Challenges And Opportunities ◽  
Scale Characterization

Protected areas (PAs) are a key strategy to reverse global biodiversity declines, but they are under increasing pressure from anthropogenic activities and concomitant effects. Thus, the heterogeneous landscapes within PAs, containing a number of different habitats and ecosystem types, are in various degrees of disturbance. Characterizing habitats and ecosystems within the global protected area network requires large-scale monitoring over long time scales. This study reviews methods for the biophysical characterization of terrestrial PAs at a global scale by means of remote sensing (RS) and provides further recommendations. To this end, we first discuss the importance of taking into account the structural and functional attributes, as well as integrating a broad spectrum of variables, to account for the different ecosystem and habitat types within PAs, considering examples at local and regional scales. We then discuss potential variables, challenges and limitations of existing global environmental stratifications, as well as the biophysical characterization of PAs, and finally offer some recommendations. Computational and interoperability issues are also discussed, as well as the potential of cloud-based platforms linked to earth observations to support large-scale characterization of PAs. Using RS to characterize PAs globally is a crucial approach to help ensure sustainable development, but it requires further work before such studies are able to inform large-scale conservation actions. This study proposes 14 recommendations in order to improve existing initiatives to biophysically characterize PAs at a global scale.

Large scale characterization of plant plasma membrane proteins

Biochimie ◽  
1999 ◽  
Vol 81 (6) ◽  
pp. 655-661 ◽  
Author(s):  
Véronique Santoni ◽  
Patrick Doumas ◽  
David Rouquié ◽  
Monique Mansion ◽  
Thierry Rabilloud ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Large Scale ◽  
Plasma Membrane Proteins ◽  
Scale Characterization ◽  
Plant Plasma Membrane

scholarly journals Semantic discrimination of technicality in French nominalizations

2020 ◽  
Vol 4 (2) ◽  
pp. 100-119
Author(s):  
Marine Wauquier ◽  
Nabil Hathout ◽  
Cécile Fabre
Keyword(s):  
Statistical Modeling ◽  
Large Scale ◽  
Distributional Analysis ◽  
Lexical Resources ◽  
Definition Of ◽  
Semantic Distinction

Abstract French suffixations in -age, -ion and -ment are considered roughly equivalent, yet some differences have been pointed out regarding the semantics of the resulting nominalizations. In this study, we confirm the existence of a semantic distinction between them on the basis of a large scale distributional analysis. We show that the distinction is partially determined by the degree of technicality of the denoted action: -age nominals tend to be more technical than -ion ones. We examine this hypothesis through the statistical modeling of technicality. To this end, we propose a linguistic definition of technicality, which we implement using empirical, quantitative criteria estimated in corpora and lexical resources. We show to what extent the differences with respect to these criteria adequately approximate technicality. Our study indicates that this definition of technicality, while amendable, provides new perspectives for the characterization of action nouns.

scholarly journals Functional characterization of 3D protein structures informed by human genetic diversity

2019 ◽  
Vol 116 (18) ◽  
pp. 8960-8965 ◽  
Author(s):  
Michael Hicks ◽  
Istvan Bartha ◽  
Julia di Iulio ◽  
J. Craig Venter ◽  
Amalio Telenti
Keyword(s):  
Large Scale ◽  
Functional Characterization ◽  
Protein Structures ◽  
Large Scale Data ◽  
Allosteric Sites ◽  
Missense Variation ◽  
Binding Pockets ◽  
Definition Of ◽  
Scale Data

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. Structural intolerance data correlated with deep mutational scanning functional readouts for PPARG, MAPK1/ERK2, UBE2I, SUMO1, PTEN, CALM1, CALM2, and TPK1 and with shallow mutagenesis data for 1,026 proteins. The 3D structural intolerance analysis revealed different features for ligand binding pockets and orthosteric and allosteric sites. Large-scale data on human genetic variation support a definition of functional 3D sites proteome-wide.

A comparative study of greywater from domestic and public buildings

2013 ◽  
Vol 14 (1) ◽  
pp. 135-141 ◽  
Author(s):  
C. Santos ◽  
C. Matos ◽  
F. Taveira-Pinto
Keyword(s):  
Urban Areas ◽  
Large Scale ◽  
Potable Water ◽  
Cost Effective ◽  
Public Buildings ◽  
Correct Definition ◽  
Cost Effective Treatment ◽  
Negative Impacts ◽  
Definition Of

Greywater (GW) can be an important resource for urban water consumption, replacing potable water for purposes that do not require drinking water quality. If applied on a large scale, this practice will reduce the potable water demand and the wastewater produced in urban areas, minimizing the negative impacts and costs of water extraction and wastewater treatment. A correct characterization of GW is important to assess its potential for a direct reuse or, if not possible, to make a correct definition of a feasible and cost-effective treatment system. This article aims to contribute to the characterization of GW produced in washbasins and showers in domestic and public buildings. A compilation of several works on GW collection and sampling produced by the authors is presented. Samples were taken from GW produced in showers and washbasins in households, changing rooms and in a restaurant. Results are compared with values presented in similar studies and compared with standards and guidelines published in different countries.

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