BUSCADOR RECOLECTA

Proposal template to be used in data requests., Peer reviewed

The folder contains a metadata sheet describing the datasets included in the LOTVS collection, and a proposal template to be used in data requests. Metadata will be regularly updated., Peer reviewed

10980_2021_1388_MOESM1_ESM = APPENDIX S1. Overview, Design concepts, and Details protocol of the individual-based model used in this study (ODD). 10980_2021_1388_MOESM2_ESM = APPENDIX S2. Description of the study areas suffering habitat transformations. 10980_2021_1388_MOESM3_ESM = APPENDIX S3. Model parameterisation based on empirical data and bibliographic review on Testudo graeca and T. hermanni. 10980_2021_1388_MOESM4_ESM = APPENDIX S4. Script in R for the calculation of stable age distribution. 10980_2021_1388_MOESM5_ESM = Supplementary material. Tables S1., Peer reviewed

Supplementary data 1. Crystallographic data for the structural analysis have been deposited on the Cambridge Crystallographic data Center (CCDC 1514267), and copies of the data can be obtained free of charge at www.ccdc.cam.ac.uk/conts/retrieving.html. Additional experimental details, structural characterization data (Projection along the a-axis showingthe polymeric an 1-D endless inorganic chain, projection of the structure of [C6H16N2O]2+ cation along the a-axis showing the chair conformation of piperazinium entities, contributions to the Hirshfeld surface area for C6H16N2OPbCl4 and model for the formation and recombination of the exciton in the title compound are given in Fig S1–S4 and selected bond distances and angles in [C6H16N2O]PbCl4 and surface composition (in atomic %) are given in Table S1 and S2.), Peer reviewed

Supplementary crystallographic data for this article in CIF format are available at the Electronic Supplementary Publication from Cambridge Crystallographic Data Centre (CCDC 1560010). This data can be obtained free of charge via http://www.ccdc.cam.ac.uk/conts/retrieving.html, from the Cambridge Crystallographic Data Centre, 12 Union Rood, Cambridge CB2 1EZ, UK (Fax: (international): +44 1223/336 033; e-mail: deposit@ ccdc.cam.ac.uk). Projection along the b-axis showing the organic-inorganic layers in the title compound crystal, relative contributions to the Hirshfeld surface areas for the various intermolecular contacts, are given in Fig S1-S2 and selected bond distances and angles in (C5H14N2)2[SnCl6]2·5H2O and Surface composition (in atomic %) are given in Table S1 and S2., Peer reviewed

The origin of the FtsZ/tubulin protein family was extremely relevant for life since these proteins are present in nearly all organisms, carrying out essential functions such as cell division or forming a major part of the cytoskeleton in eukaryotes. Therefore, investigating the early evolution of the FtsZ/tubulin protein family could reveal crucial aspects of the diversification of the three domains of life. In this study, we revisited the phylogenies of the FtsZ/tubulin protein family in an extensive prokaryotic diversity, focusing on the main evolutionary events that occurred during its evolution. We found evidence of its early origin in the last universal common ancestor since FtsZ was present in the last common ancestor of Bacteria and Archaea. In bacteria, ftsZ genes are genomically associated with the bacterial division gene cluster, while in archaea, ftsZ duplicated prior to archaeal diversification, and one of the copies is associated with protein biosynthesis genes. Archaea have expanded the FtsZ/tubulin protein family with sequences closely related to eukaryotic tubulins. In addition, we report novel CetZ-like groups in Halobacterota and Asgardarchaeota. Investigating the C-termini of prokaryotic paralogs basal to eukaryotic tubulins, we show that archaeal CetZ, as well as the plasmidic TubZ from Firmicutes, most likely originated from archaeal FtsZ. Finally, prokaryotic tubulins are restricted to Odinarchaeaota and Prosthecobacter species, and they seem to belong to different molecular systems. However, their phylogenies suggest that they are closely related to α/β-tubulins pointing to a potential ancestrality of these eukaryotic paralogs of tubulins, Peer reviewed

This file describes meteorological and limnological methodologies used by the author to obtain data from Las Madres lake and its environment in 1991-2021., Peer reviewed

This file compiles supplementary materials of the book on the long-term limnology of Las Madres lake (Spain) for 1991-2021., Peer reviewed

[Description of methods used for collection/generation of data] Auditory function (ABR data): Auditory brainstem responses (ABR) recordings were performed on a TDT ABR and DPOAE acquisition system, with a RZ6 processor (Tucker‐Davis Technologies, Alachua, FL, USA). In brief, mice were anesthetized with ketamine (100 mg/kg; Imalgene 1000; Merial, Lyon, France) and xylazine (10 mg/kg; Rompun 2%; Bayer, Leverkusen, Germany) by intraperitoneal injection and the ABR tests were performed in a sound‐attenuating chamber. Two different sound stimuli, clicks and tone bursts, were generated with SigGenRZ software (TDT). Stimuli were calibrated using SigCalRZ software and a PCB 377C01 precision condenser microphone, with a 426B03 preamplifier and a 480C02 signal conditioner. Click (duration 0.1 ms) and tone burst (duration 5 ms, 2.5 ms each for rise and decay, without plateau) at 4, 8, 16, 24, 32 and 40 kHz stimuli were delivered by a MF1 open field magnetoelectrostatic speaker (TDT) at 30 (click) or 50 (tone bursts) pulses per second, and from 90 to 10 dB SPL, in 5–10 dB steps. The evoked response was collected with stainless steel needle electrodes placed at the vertex (active), ventrolateral to the right ear (reference) and tail base (ground), promediated, and analyzed with BioSigRZ software (TDT). Cochlear gene expresión: Inner ear dissection was performed and samples were frozen in RNAlater® solution (Ambion, Foster City, CA, USA). Cochlear RNA was extracted using the RNeasy Plus Mini kit (Qiagen, Hilden, Germany) automated on the Qiacube (Qiagen, Hilden, Germany). Quality determination and cDNA generation from pooled cochlear RNA extracts (3 cochlea from different animals per group) were performed. Quantitative amplification was performed in triplicate on a Quant Studio 7 Flex PCR System (Applied Biosystems, Foster City, CA, USA) using either commercial TaqMan probes (Nox4, Nox3, Nrf2, Nlrp3, Il1b, Tnfa). Data were collected after each amplification step and analyzed with QuantStudio™ Real-Time PCR software 1.3 (Applied Biosystems). Hprt1 gene was used as a housekeeping gene, and the n-fold differences were calculated using the 2−ΔΔCt method., The objective of the study was to explore the role of NOX4 in agen-related hearing loss. Hearing evaluation (with auditory brainstem responses, ABR) and cochlear gene expresión in Nox4 knockout mice compared to wild type mice, along age (2-15 months). ABR data were obtained from Nox4 knockout and wild type mice fom 2 to 15 month of age. Cochlear expression of Nox3, Nox4, Nrf2, Nlrp3, Il1b and Tnfa genes were determined by RT-qPCR in pooled simples (3 cochleae from 3 independent mice) in Nox4 knockout and wild type of 4 and 8 months of age., THEARPY: bases genéticas y moleculares de la sordera neurosensorial y del daño auditivo: exploración de nuevas dianas y estrategias terapéuticas”. Convocatoria 2020 Proyectos de I+D+i - RTI Tipo B (PID2020-115274RB-I00). FEDER/MICIN, 2021-2024., ABR DATA: - Folder with .arf files, raw data from Auditory Brainstem Response test performed by a Tucker Davis Technologies Workstation in Nox4 knockout and wiild type littermates at different ages from 2 to 15 months. - Folder with cvs files, processed data with ABR waves analysis. - SPSS file, including all the data used for statistics. GENE EXPRESIION DATA: -pdf file with RNA integrity data. Samples consisted on pools of 3 cochleae per genotype (Nox4 knockout and wiild type) and age (4 and 8 months) -Excel file with gene expresión data, using two endogenous genes (Rplp0 and Hprt1)., Peer reviewed

Suppl. Fig S1. Comparison of length and number of substitutions versus p-value in the calculation of the Ka/Ks ratio. Genes have been colored according to the group to which they belong. A regression line has been added, together with its correlation coefficient and associated p-value. Suppl. Fig S2. Distribution of Ka/Ks along the length of genes S, M, N and E (black line). The normalized Shannon entropy obtained from Nextstrain database is shown for comparison (https://nextstrain.org/ncov/gisaid/global/6m). Pfam domains have been included (below): S → bCovS1N (PF16451, Betacoronavirus-like spike glycoprotein S1, N-terminal), bCoV_S1_RBD (PF09408, Betacoronavirus spike glycoprotein S1, receptor binding), CoV_S1_C (PF19209, Coronavirus spike glycoprotein S1, C-terminal), CoV_S2 (PF01601, Coronavirus spike glycoprotein S2); M → CoVM (PF01635, Coronavirus M matrix/glycoprotein); N → bCoV_lipid_BD (PF09399, Betacoronavirus lipid binding protein), bCoV_Orf14 (PF17635, Betacoronavirus uncharacterised protein 14), CoV_nucleocap (PF00937, Coronavirus nucleocapsid); E → CoVE (PF02723, Coronavirus small envelope protein E). The blue line marks the Ka/Ks value of 1. Suppl. Table S1. Genomes used in this work. Suppl. Table S2. Ka/Ks ratio obtained for each SARS-CoV-2 gene, together with the associated p-value. Blue color highlights structural genes, red color highlights non-structural genes, and gray color highlights accessory factors., The SARS-CoV-2 virus pandemic that emerged in 2019 has been an unprecedented event in international science, as it has been possible to sequence millions of genomes, tracking their evolution very closely. This has enabled various types of secondary analyses of these genomes, including the measurement of their sequence selection pressure. In this work we have been able to measure the selective pressure of all the described SARS-CoV-2 genes, even analyzed by sequence regions, and we show how this type of analysis allows us to separate the genes between those subject to positive selection (usually those that code for surface proteins or those exposed to the host immune system) and those subject to negative selection because they require greater conservation of their structure and function. We have also seen that when another gene with an overlapping reading frame appears within a gene sequence, the overlapping sequence between the two genes evolves under a stronger purifying selection than the average of the non-overlapping regions of the main gene. We propose this type of analysis as a useful tool for locating and analyzing all the genes of a viral genome, when an adequate number of sequences are available., Peer reviewed