No difference in plasticity between different ploidy levels in the Mediterranean herb Mercurialis annua.

Increased phenotypic plasticity for a number of plant traits has been suggested as a possible reason for the success and spread of polyploids. One such trait is a plant's sex allocation (or gender), which influences its reproductive success directly as a function of the potentially heterogeneous mating prospects in the population. However, it is unknown how polyploidy per se might affect plasticity in a plant's sex allocation. Although there have been numerous comparisons between diploid and (usually) tetraploid taxa, we know very little about how elevated ploidy above the diploid level might affect plasticity. Here, we ask whether different ploidy levels > 2x express different plasticity in the ruderal plant Mercurialis annua. We grew tetraploid and hexaploid hermaphrodites under different levels of nutrient availability and compared their reaction norms for growth (above-ground biomass, SLA) and reproductive traits (reproductive effort, phenotypic gender). Overall, we found that an increase in ploidy level from 4x to 6x in M. annua is associated with an increase in the relative biomass allocated to seeds, measured as female reproductive effort. However, our study provides no support for the idea that increasing ploidy level increases the ability to express different phenotypes in response to changes in the environment

Advances in xmipp for cryo-electron microscopy: From xmipp to scipion

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package

Sex-Differential Herbivory in Androdioecious Mercurialis annua

Males of plants with separate sexes are often more prone to attack by herbivores than females. A common explanation for this pattern is that individuals with a greater male function suffer more from herbivory because they grow more quickly, drawing more heavily on resources for growth that might otherwise be allocated to defence. Here, we test this ‘faster-sex’ hypothesis in a species in which males in fact grow more slowly than hermaphrodites, the wind-pollinated annual herb Mercurialis annua. We expected greater herbivory in the faster-growing hermaphrodites. In contrast, we found that males, the slower sex, were significantly more heavily eaten by snails than hermaphrodites. Our results thus reject the faster-sex hypothesis and point to the importance of a trade-off between defence and reproduction rather than growth

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewedThe authors would like to acknowledge support from the Spanish Ministry of Economy and Competitiveness through grants BIO2013-44647-R and BIO2016-76400-R (AEI/ FEDER, UE), Comunidad Autonoma de Madrid through grant S2017/BMD-3817, Instituto de Salud Carlos III through grants PT13 /0001/0009 and PT17/0009/0010,the European Union (EU) and Horizon 2020 through West-Life (EINFRA- 2015-1, Proposal 675858), CORBEL (INFRADEV-1-2014-1, Proposal 654248), ELIXIR–EXCELERATE (INFRADEV-3- 2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and the National Institutes of Health (P41 GM 103712) (IB

Electronic consequences of chemical doping of 7-Armchair Graphene Nanoribbons

Resumen del trabajo presentado a la International Conference on Nanoscience + Technology (ICN+T), celebrada en Brno (Czech Republic) del 22 al 27 de julio de 2018.The tunable electronic structure of Graphene Nanoribbons (GNRs) with different edge types has provoked great interest due to potential applications in electronic devices as molecular diodes or transistors. Thanks to the on-surface synthesis of chemically customized molecular precursors, nanoribbons with atomically defined structure can be grown. This high precision in their bottom-up growth allows to tune their electronic structure via width control or chemical doping. Here we use two different strategies to chemically modify 7-armchair GNRs (7-AGNRs) to clarify how the chemical modifications on the nanoribbons’ structure affect their electronic properties. By means of Scanning Tunneling Spectroscopy we tackle with atomic precision this issue on 7-AGNRs with substitutional nitrile functional groups at the ribbons’ edges and on 7-AGNRs with substitutional boron atoms within the ribbons’ backbone. We find that in the first case the CN groups lead to an efficient n-like doping of the ribbon, while in the second case B atoms induce the formation of a new acceptor band and bandgap renormalization.Peer Reviewe

Flexible workflows for on-the-fly electronmicroscopy single-particle image processing using Scipion

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data setThe authors would like to acknowledge financial support from The Spanish Ministry of Economy and Competitiveness through the BIO2016-76400-R (AEI/FEDER, UE) grant, the Comunidad Auto´noma de Madrid through grant S2017/BMD3817, the Instituto de Salud Carlos III (PT17/0009/0010), the European Union (EU) and Horizon 2020 through the CORBEL grant (INFRADEV-1-2014-1, Proposal 654248), the ‘la Caixa’ Foundation (ID 100010434, Fellow LCF/BQ/ IN18/11660021), Elixir–EXCELERATE (INFRADEV-3- 2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and INSTRUCT–ULTRA (INFRADEV03-2016-2017, Proposal 731005

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achievedWe acknowledge support from “la Caixa” Foundation (Fellowship LCF/BQ/DI18/11660021. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 713673. We also thank the financial support from the Spanish Ministry of Economy and Competitiveness through Grants BIO2016-76400-R(AEI/FEDER, UE) and SEV 2017-0712, the “Comunidad Autónoma de Madrid” through Grant: S2017/BMD-3817, Instituto de Salud Carlos III, PT17/ 0009/0010 (ISCIII-SGEFI/ERDF), European Union (EU) and Horizon 2020 through grants: CORBEL (INFRADEV-1-2014-1, Proposal: 654248), INSTRUCT-ULTRA (INFRADEV-03-2016-2017, Proposal: 731005), EOSC Life (INFRAEOSC-04-2018, Proposal: 824087), High- ResCells (ERC-2018-SyG, Proposal: 810057), IMpaCT (WIDESPREAD-03-2018 – Proposal: 857203), EOSC-Synergy (EINFRA-EOSC-5, Proposal: 857647), and iNEXT-Discovery (Proposal: 871037). The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI projec

INRISCO: INcident monitoRing in Smart COmmunities

Major advances in information and communication technologies (ICTs) make citizens to be considered as sensors in motion. Carrying their mobile devices, moving in their connected vehicles or actively participating in social networks, citizens provide a wealth of information that, after properly processing, can support numerous applications for the benefit of the community. In the context of smart communities, the INRISCO [1] proposal intends for (i) the early detection of abnormal situations in cities (i.e., incidents), (ii) the analysis of whether, according to their impact, those incidents are really adverse for the community; and (iii) the automatic actuation by dissemination of appropriate information to citizens and authorities. Thus, INRISCO will identify and report on incidents in traffic (jam, accident) or public infrastructure (e.g., works, street cut), the occurrence of specific events that affect other citizens' life (e.g., demonstrations, concerts), or environmental problems (e.g., pollution, bad weather). It is of particular interest to this proposal the identification of incidents with a social and economic impact, which affects the quality of life of citizens.This work was supported in part by the Spanish Government through the projects INRISCO under Grant TEC2014-54335-C4-1-R, Grant TEC2014-54335-C4-2-R, Grant TEC2014-54335-C4-3-R, and Grant TEC2014-54335-C4-4-R, in part by the MAGOS under Grant TEC2017-84197-C4-1-R, Grant TEC2017-84197-C4-2-R, and Grant TEC2017-84197-C4-3-R, in part by the European Regional Development Fund (ERDF), and in part by the Galician Regional Government under agreement for funding the Atlantic Research Center for Information and Communication Technologies (AtlantTIC)

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded

Genomic Characterization of Host Factors Related to SARS-CoV-2 Infection in People with Dementia and Control Populations: The GR@ACE/DEGESCO Study

Emerging studies have suggested several chromosomal regions as potential host genetic factors involved in the susceptibility to SARS-CoV-2 infection and disease outcome. We nested a COVID-19 genome-wide association study using the GR@ACE/DEGESCO study, searching for susceptibility factors associated with COVID-19 disease. To this end, we compared 221 COVID-19 confirmed cases with 17,035 individuals in whom the COVID-19 disease status was unknown. Then, we performed a meta-analysis with the publicly available data from the COVID-19 Host Genetics Initiative. Because the APOE locus has been suggested as a potential modifier of COVID-19 disease, we added sensitivity analyses stratifying by dementia status or by disease severity. We confirmed the existence of the 3p21.31 region (LZTFL1, SLC6A20) implicated in the susceptibility to SARS-CoV-2 infection and TYK2 gene might be involved in COVID-19 severity. Nevertheless, no statistically significant association was observed in the COVID-19 fatal outcome or in the stratified analyses (dementia-only and non-dementia strata) for the APOE locus not supporting its involvement in SARS-CoV-2 pathobiology or COVID-19 prognosis