BUSCADOR RECOLECTA

Table S1. Checklist of items according to STROBE document. Table S2. Definitions of the key variables used. Table S3. Summary of outcomes for the different analyses. Table S4. Characteristics of patients who underwent debridement, antibiotic therapy, and implant retention (DAIR) treated with and without rifampicin. Table S5. Approval of the ethics committee of all participating centers. Figure S1. Cumulative proportion of SA-PJIs occurring after primary arthroplasty., Peer reviewed

Resources available on the publisher's site: https://doi.org/10.5281/zenodo.5554758, Streptococcal pyrogenic exotoxin B (SpeB) is a cysteine protease expressed during group A streptococcal infection that represents a major virulence factor. Although subject to several studies, its role during infection is still under debate, and its proteolytic properties remain insufficiently characterized. Here, we revisited this protease through a set of complementary approaches relying on state of-the-art HPLC-MS methods. After conceiving an efficient protocol to recombinantly express SpeB, the zymogen of the protease and its activation were characterized. Employing proteome-derived peptide libraries, a strong preference for hydrophobic and aromatic residues at P2 alongside negatively charged amino acids at P3′ to P6′ was revealed. To identify relevant in vivo substrates, native proteins were obtained from monocytic secretome and plasma to assess their cleavage under physiological conditions. Besides corroborating our findings concerning specificity, more than 200 cleaved proteins were identified, including proteins of the extracellular matrix, proteins of the immune system, and proteins involved in inflammation. Finally, the cleavage of IgG subclasses was studied in detail. This study precisely depicts the proteolytic properties of SpeB and provides a library of potential host substrates, including their exact cleavage positions, as a valuable source for further research to unravel the role of SpeB during streptococcal infection., Peer reviewed

[Description of methods used for collection/generation of data] The long-term monitoring of Doñana’s diurnal butterflies is part of a harmonised protocol of the Long-term Ecological Monitoring Program of Natural Resources and Processes. The general aim of this protocol is to monitor and assess the dynamics of diurnal butterflies (Papilionoidea) of Doñana. This group of insects is suitable to include in a monitoring protocol, for several reasons: a relative easy identification, it is a good group as bioindicators due to their short life cycle and their high sensitivity to climate, and their relation with plants allow relate their presence with vegetation changes.The monitoring of diurnal butterflies (Papilionoidea) in Doñana, southwestern Spain, was initiated in 2005, but until 2007 the protocol is not well stablished, that is why the temporal range of this dataset start in december of 2007 with one transect. From this first transect, in 2008 the Monitoring Program of Natural Resources and Processes applied the BMS methodology to new zones and transects. The principals aims of this protocol were: to inventory all species of diurnal butterflies that inhabits in Doñana, in order to detect the appearance of new species or the local extinction of some populations; and know the dynamics and variations of butterflies populations between years and between months, in order to detect declines in these animal populations. Following the Butterfly Monitoring Scheme (BMS) and Pollard's transects, the data collection is based in walking transect of a determinate distance where the observer must note, count and identify (when is possible also sex) all butterflies that fly in an imaginary cube of 5 meters of side. In the period 2007-2013, the data was collected with the software CyberTracker and all the butterflys occurences have a coordinate associated; but since 2014 the data collection was changed to BMS that is why individuals recorded in this period (2014-2022) did not have a coordinate. The transect was adapted to optimal period of butterflies' day activity, that is three or four hours before and after noon, always with suitable climatic conditions: no rain and/or fog, minimum temperature between 13 on sunny days and 17ºC on cloudly days, maximum temperature below 30 ºC and wind conditions under 5 in Beaufort's scale. In order to know environmental and meteorological variables, temperature, wind conditions (Beaufort's scale) and cloud coverage (eighths of coverage) were measured at initial and final of each transect. The distance of transects varies between 460 and 1170 metres. The time to complete the transects varies depending on the number of individuals observed in each one, but time values are usually between 10 and 75 minutes., Dataset are structured following well-established data formats. Three files are provided and they are related to each other with the variable eventID. The first file (icts-rbd-butterfly_ev_20230717) contains the information of each transect (time of occurrence, geographical and topographical information, sampling effort, etc…); the second file (icts-rbd-butterfly_occ_20230717) contains the abundance of each butterfly species recorded in each sampling event, numbers of individual recorded and taxonomic classification; the third file (icts-rbd-butterfly_mof_20230717) contains additional information (measurements or facts) of meteorological information (temperature, wind conditions and cloud coverage) recorded in each sampling event and habitat information of each transect., The data from 2014 to present is accessible in European Butterfly Monitoring Scheme (eBMS) https://butterfly-monitoring.net/, The long-term monitoring of Doñana’s diurnal butterflies is part of a harmonised protocol of the Long-term Ecological Monitoring Program of Natural Resources and Processes. The general aim of this protocol is to monitor and assess the dynamics of diurnal butterflies (Papilionoidea) of Doñana (Paz et al., 2014).. This group of insects is suitable to include in a monitoring protocol, for several reasons: a relative easy identification, it is a good group as bioindicators due to their short life cycle and their high sensitivity to climate, and their relation with plants allow relate their presence with vegetation changes. The monitoring of diurnal butterflies (Papilionoidea) in Doñana, southwestern Spain, was initiated in 2005, but until 2007 the protocol is not well stablished, that is why the temporal range of this dataset start in december of 2007 with one transect. From this first transect, in 2008 the Monitoring Program of Natural Resources and Processes applied the BMS methodology to new zones and transects. The principals aims of this protocol were: to inventory all species of diurnal butterflies present in Doñana, in order to detect the appearance of new species or the local extinction of some populations; and know the dynamics and variations of butterflies populations between years and between months, in order to detect declines in these animal populations. Following the Butterfly Monitoring Scheme (BMS) and Pollard's transects (Sevilleja et al., 2019), the data collection is based in walking transect of a determinate distance where the observer must note, count and identify (when is possible also sex) all butterflies that fly in an imaginary cube of 5 meters of side. The transects are divided into sections with a different or equal length, that usually correspond to different habitat areas. These sections are related to the EUNIS habitat classification (version 2012) and to SACRE habitat classification. In the period 2007-2013, the data was collected with the software CyberTracker and all the butterflys occurences have a coordinate In the period 2007-2013, the data was collected with the software CyberTracker and all the butterflys occurences have a coordinate associated; but since 2014 the data collection was changed to BMS that is why individuals recorded in this period (2014-2022) did not have a coordinate. The transect was adapted to optimal period of butterflies' day activity, that is three or four hours before and after noon, always with suitable climatic conditions: no rain and/or fog, minimum temperature between 13 on sunny days and 17ºC on cloudly days, maximum temperature below 30 ºC and wind conditions under 5 in Beaufort's scale. In order to know environmental and meteorological variables, temperature, wind conditions (Beaufort's scale) and cloud coverage (eighths of coverage) were measured at initial and final of each transect. The distance of transects varies between 460 and 1170 metres. The time to complete the transects varies depending on the number of individuals observed in each one, but time values are usually between 10 and 75 minutes. References: Paz, D., Román, J y Janss, G. (2014) Protocolo de muestreo 3: Censo de mariposas diurnas (Ropalóceros) mediante transectos fijos en el Espacio Natural de Doñana. Documentos Técnicos del Equipo de Seguimiento de Recursos y Procesos Naturales. ICTS-Reserva Biológica de Doñana. Estación Biológica de Doñana (CSIC). Sevilleja, C.G., van Swaay, C.A.M., Bourn, N., Collins, S., Settele, J., Warren, M.S., Wynhoff, I. and Roy, D.B. (2019). Butterfly Transect Counts: Manual to monitor butterflies. Report VS2019.016, Butterfly Conservation Europe & De Vlinderstichting/Dutch Butterfly Conservation, Wageningen. EUNIS Habitat Classification, https://eunis.eea.europa.eu/ Programa SACRE, https://www.miteco.gob.es/es/parques-nacionales-oapn/red-parques-nacionales/seguimiento/seguimiento-ecologico/aves.aspx, We acknowledge financial support from National Parks Autonomous Agency (OAPN) between 2004-2007; Singular Scientific and Technical Infrastructures from the Spanish Science and Innovation Ministry (ICTS-MICINN); Ministry of Agriculture, Livestock, Fisheries and Sustainable Development from the Regional Government of Andalusia (CAGPDES-JA) since 2007; and Doñana Biological Station from the Spanish National Research Council (EBD-CSIC) since all the study period (2007-2022). This monitoring protocol has been assigned to European Butterfly Monitoring Scheme (eBMS) since 2014., Peer reviewed

Supplementary Table S1. Yeast strains used in this study. Supplementary Table S2. Plasmids used in this study. Supplementary Table S3. Oligonucleotides used in this study. Supplementary Figure S1. Pre-rRNA processing in S. cerevisiae. Supplementary Figure S2. The nascent polypeptide exit tunnel is comprised of rRNA and three r-proteins uL4, uL22, and eL39. Supplementary Figure S3. The rpl39 D mutant exhibits a slow growth phenotype, enhanced at low temperatures. Supplementary Figure S4. eL39 is required for biogenesis of 60S r-subunits. Supplementary Figure S5. Wild-type and GFP-tagged eL39 complement the rpl39 D mutant. Supplementary Figure S6. The absence of eL39 leads to nuclear retention of pre-60S r-subunits, which is exaggerated in the cold. Supplementary Figure S7. Simplified pre-60S r-subunit assembly pathway. Supplementary Figure S8. Only partial densities for eL39 are visualized in the state E particles. Supplementary Figure S9. eL39 protein assembles in the nucleolus. Supplementary Figure S10. Accumulation of 27S and 7S pre-rRNAs in the absence of eL39 is not dependent on the presence of the TRAMP component Trf4 and the nuclear exosome component Rrp6. Supplementary Figure S11. Nog2-associated particles do not accumulate early assembling/early dissociating AFs in cells expressing rpf2 D255-344. References., Peer reviewed

Additional file 1: Table ST1. Treatments comparison by outcome in male patients. Table ST2. Treatments comparison by outcome in female patients. Table ST3. WHO classification of disease outcome. Table ST4. Panels and antibodies used for immunophenotyping. Figure SF1. Patients distribution by outcome, age, and comorbidities. Figure SF2. Distribution of male patients with comorbidities according to age and testosterone levels. Figure SF3. Longitudinal analysis of serum levels of IL-6, C-reactive protein (CRP), ferritin and lactate dehydrogenase (LDH) in male patients. Figure SF4. Bioavailable testosterone serum levels and correlation between age and sex-hormone binding globulin (SHBG). Figure SF5. Flow cytometry analysis of circulating immune subpopulations in three illustrative cases with moderate, severe survivor and severe deceased outcomes., Ministerio de Ciencia, Innovación y Universidades Consejo Superior de Investigaciones Científicas Agència de Gestió d’Ajuts Universitaris i de Recerca Conselleria d'Educació, Investigació, Cultura i Esport Instituto de Salud Carlos III, Peer reviewed

Document S1. Figures S1–S5. Table S1. Ranked list of co-translational SecB substrates, related to Figure 1. Table contains rank, gene name, coverage (number of reads in the total translatome divided by gene length), low_CI (see STAR Methods for details), and subcellular localization. Table S2. Protein quantification of SecB-bound RNCs compared with all ribosomes, related to Figure 1. Table contains UniProt identifier, LFQ intensities of quantified proteins, and protein descriptors (name, biological function, biological processes). Table S3. Ranked list of co-translational SecB substrates in Δtig background, related to Figure 6. Table contains rank, gene name, coverage (number of reads in the total translatome divided by gene length), low_CI (see STAR Methods for details), and subcellular localization. Document S2. Article plus supplemental information., Peer reviewed

Table 1. Complete list of epitomes., [Background] The fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion., [Methods] The analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses., [Results] Our data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2., [Conclusions] These mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses., Peer reviewed

Figure S1 Proteolytic activity of proteases (inactive zymogen proBFT-3, trypsin-activated BFT-3, and trypsin). Figure S2 Overview representation of all proBFT-3 structures determined. Figure S3 Close-up views of the inhibitor-binding exosite, the identified protein-ligand interaction network, and the proteolytic active site. Figure S4 Molecular representation of the identified BFT-3 exosite inhibitors. Figure S5 Ligand-omitted and bulk solvent-excluding mFo–DFc electron density maps of the identified exosite inhibitors. Figure S6 Size-exclusion chromatography (SEC) of proBFT-3 prior protein crystallization experiments. Table S1 Primary and secondary antibodies. Table S2 Crystallographic data. Table S3 Therapeutic information for the identified compounds. Table S4 Dissociation constants of the activated BFT-3-compound complexes obtained by ITC at 25°C and pH 7.4., Peer reviewed

S1 File. List of participating centers., Peer reviewed

S2 File. Definitions for main trial variables., Peer reviewed