BUSCADOR RECOLECTA

Ecological Niche Modelling output and input., PID2019-107078GB-I00 funded by MCIN/AEI/10.13039/501100011033. 2017-SGR-991 funded by Generalitat de Catalunya. BES-2017-080641 funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”., Peer reviewed

Sample Processing Protocol Cells were mock treated or UV-C irradiated (20 J/m2) and harvested after 1 h. Cell pellets were lysed for 20 min on ice in EBC-150 buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5 % NP-40, 2 mM MgCl2, protease inhibitor cocktail (Roche)) supplemented with 500 U/mL Benzonase® Nuclease (Novagen). Cell lysates were incubated for 1.5 h at 4°C with GFP-Trap®_A beads (Chromotek). The beads were then washed six times with EBC-150 buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5 % NP-40, 1 mM EDTA, protease inhibitor cocktail (Roche), 5 time ammonium bicarbonate 50mM. and Trypsinized overnight. Peptides were later analysed by mass spectrometry. Data Processing Protocol Mass spectrometry was performed essentially as previously described . Samples were analyzed on a Q-Exactive Orbitrap mass spectrometer (Thermo Scientific, Germany) coupled to an EASY-nanoLC 1000 system (Proxeon, Odense, Denmark). Digested peptides were separated using a 20 cm fused silica capillary (ID: 75 µm, OD: 375 µm, Polymicro Technologies, California, US) in-house packed with 1.9 µm C18-AQ beads (Reprospher-DE, Pur, Dr. Maisch, Ammerburch-Entringen, Germany). Peptides were separated by liquid chromatography using a gradient from 2 % to 30 % acetonitrile in 0.1% formic acid. For the ALC1 samples and related GFP controls the gradient length was 40 min. For the XPC,PARP1 and PARP2 samples grandient length was 100 min. Every gradient was followed by an increase to 95% acetonitrile and back to 2% acetonitrile in 0.1% formic acid for chromatography column re-conditioning. Flow rate of was set 200 nl/min for 2 h. The mass spectrometer was operated in positive-ion mode at 2.8 kV with the capillary heated to 250°C. Data-dependent acquisition mode was used to automatically switch between full scan MS and MS/MS scans, employing a top 7 method. Full scan MS spectra were obtained with a resolution of 70.000, a target value of 3x106 and a scan range of 400-2.000 m/z (XPC samples) or 300-1600 m/z (ALC1, PARP1 and PARP2 samples). Higher-Collisional Dissociation (HCD) tandem mass spectra (MS/MS) were recorded with a resolution of 35,000, a target value of 1x105 and a normalized collision energy of 25%. The precursor ion masses selected for MS/MS analysis were subsequently dynamically excluded from MS/MS analysis for 60s and Precursor ions with a charge state of 1 and greater than 6 were excluded from triggering MS/MS events. Maximum injection times for MS and MS/MS were 20 and 120 ms (XPC) or 250 and 120 ms (ALC1, PARP1 and PARP2), respectively. Mass spectrometry data analysis. All raw data were analyzed using MaxQuant (version 1.6.6.0) as described previously. We performed the search against an in silico digested UniProt reference proteome for Homo sapiens including canonical and isoform sequences (27th May 2019). Database searches were performed according to standard settings with the following modifications. Digestion with Trypsin/P was used, allowing 4 missed cleavages. Oxidation (M), Acetyl (Protein N-term) were allowed as variable modifications with a maximum number of 3. Carbamidomethyl (C) was disabled as a fixed modification. Label-Free Quantification was enabled, not allowing Fast LFQ. iBAQ was calculated., Cells employ global genome DNA damage repair (GGR) to eliminate a broad spectrum of DNA lesions, including those induced by UV light. The lesion-recognition factor XPC initiates repair of helix-distorting DNA lesions, but binds inefficiently to lesions that cause poor helix distortion. How such difficult-to-repair lesions are detected in chromatin is unknown. Here, we identify the poly-(ADP-ribose) polymerases PARP1 and PARP2 as constitutive interactors of XPC. The close interaction between these proteins results in the PARylation of XPC at UV lesions, and an XPC-dependent stimulation of the poly-(ADP-ribose) response, which facilitates the recruitment of the poly-(ADP-ribose)-dependent chromatin remodeler ALC1. Both ALC1 and in particular PARP2 are required for the efficient clearing of difficult-to-repair DNA lesions. Our study offers key insights into the molecular mechanisms of GGR by revealing a molecular bookmarking system, which primes chromatin containing difficult-to-repair DNA lesions for efficient repair., Peer reviewed

Dataset: Review of Area-based management tools (ABMTs) and related legal sources from International and Regional Agreements. -- All the web links of Tab. 7 were accessed on March 9, 2020., Peer reviewed

[Usage notes] The dataset of the Atlas of mitochondrial genetic diversity for Western Palearctic butterflies (COI sequences and metadata) is available in the iodatabase R package available at https://github.com/leondap/iodatabase. Here the R script with a few supplementaty files is available in order to replicate the figures composing the Atlas, [Motivation] Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies., [Main types of variables contained] A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes., [Spatial location and grain] The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude., [Time period and grain] DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022., [Major taxa and level of measurement] Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level., [Software format] Data and functions to manage the dataset are provided in the iodatabase R package (https://github.com/leondap/iodatabase) and in Dryad., Università degli Studi di Firenze ., Peer reviewed

The dataset of the Atlas of mitochondrial genetic diversity for Western Palearctic butterflies (COI sequences and metadata) is available in the iodatabase R package available at https://github.com/leondap/iodatabase.-- Here the R script with a few supplementaty files is available in order to replicate the figures composing the Atlas., [Motivation] Butterflies represent a model in biology and a flagship group for invertebrate conservation. We provide four new resources for the Western-Palearctic butterflies: 1) An updated checklist comprising 552 species; 2) a curated dataset of 32,129 mitochondrial COI sequences for 532 species, including a de novo reference library for the Maghreb (Morocco and northern Algeria and Tunisia) and Macaronesia (Azores, Madeira and Canary Islands); 3) seven indexes of intraspecific genetic variation (IGV): observed and expected number of haplotypes, haplotype and nucleotide diversity, two fixation indexes, and maximum p-distance; 4) species-level maps illustrating the distribution of COI variability and haplotype networks. The updated checklist will be fundamental for any application dealing with butterfly diversity in Western Palearctic. IGV indexes provide measures for genetic polymorphism and spatial structure and represent proxies for dispersal capacity. These resources will facilitate comparative studies of macrogenetics, will foster integrative taxonomy, and will aid conservation strategies., [Main types of variables contained] A complete species checklist in table format, 32,129 mitochondrial DNA-barcodes provided with metadata (species membership, WGS84 coordinates, sequence length), and a book in PDF format including the IGV atlas and indexes., [Spatial location and grain] The checklist encompasses Europe up to Urals in the east, north Macaronesia (Azores, Madeira and Canary Islands), as well as the Maghreb (Morocco and northern Algeria and Tunisia). DNA-barcodes have been retained in the geographic interval of -31.3–67.5 degrees of longitude and 27.5–71.2 degrees of latitude., [Time period and grain] DNA-barcodes originate from studies published between 1998-2022 and from de novo sequencing of 2,608 specimens done between 2007-2022., [Major taxa and level of measurement] Butterflies (Lepidoptera, Papilionoidea), analysed from individual to species level., [Software format] Data and functions to manage the dataset are provided in the iodatabase R package (https://github.com/leondap/iodatabase) and in Dryad., Funding provided by: Università degli Studi di Firenze. Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100004434, Peer reviewed

The Integrated and Open Butterfly Database provide a massive dataset of curated COI sequences for West Palearctic butterflies and an updated checklist. Functions to manage the dataset are also provided., The IOdatabase is intended as a project integrating several datasets of butterflies from Western Palaearctic harmonised with a shared taxonomy. IOdatabase now includes a revised version of the species checklist from West Palerarctic (Wiemers et al. 2016 and Middleton Welling et al. 2020) and more than 30000 COI sequences for 532 species. COI sequences belong to three main sources: 1) De novo sequencing mostly for Maghreb and Macaronesia 2) Published DNA-barcode libraries and public BOLD projects compiled at regional level 3) Studies providing COI of single species or genera. In the latter case, we checked whether haplotypes, instead of specimens, were included in repositories (Paz‐Vinas et al. 2021). If the number of specimens sharing a given haplotype in a particular location was reported, we replicated the haplotype sequences to obtain data at the specimen level, otherwise the sequences were excluded. We verified species identifications by building neighbor-joining trees for each genus. When morphology could not be verified, we removed sequences not clustering within the species to which they were attributed if the mismatch did not involve one of the 74 species showing DNA-barcode sharing. Metadata are also available: coordinates in WGS84 (degrees) and Lambert projections (meters), BOLD and Genbank codes, Continental areas and country obtained by an autmatic attribution using the rworldextra R package. Using these data we also calculated some basic indexes of genetic diversity (number of haplotypes observed and predicted based on rarefaction curves, GST, DST, haplotype diversity and nucleotide diversity)., Peer reviewed

Material For modeling AlphaFold2_multimer was used. AlphaFold2 was downloaded from https://github.com/deepmind/alphafold/releases. Full length amino acid sequences of human PHF14 and HMG20A were used: >NP_001291433.1 high mobility group protein 20A isoform a [Homo sapiens] >NP_001007158.1 PHD finger protein 14 isoform 1 [Homo sapiens] To perform PHF14-HMG20A complex models we used Alphafold_multimers (v2.1.1) with --db_preset=reduced_dbs, --model_preset=multimer --max_template_date=2021-11-01, and default parameters. Computation was performed in the CESGA Supercomputing Center. RCSB PDB (https://www.rcsb.org/3d-view) or Swiss PDB viewer (DeepView) were used for structure viewing. Procedure Full lenth amino-acid protein sequences were obtained form NCBI Protein. Then, to perform PHF14-HMG20A complex models we used Alphafold_multimers (v2.1.1) with --db_preset=reduced_dbs, --model_preset=multimer --max_template_date=2021-11-01, and default parameters. A PAE plot (Predicted Aligned Error Plot) is uploaded. PAE plot "reports AlphaFold’s expected position error at residue x, when the predicted and true structures are aligned on residue y. This is useful for assessing confidence in global features, especially domain packing. For residues x and y drawn from two different domains, a consistently low PAE at (x, y) suggests AlphaFold is confident about the relative domain positions" (https://deepmind.com/research/publications/2021/enabling-high-accuracy-protein-structure-prediction-at-the-proteome-scale). A distogram (Matrix of distances between different parts of the proteins) is also uploaded., Structural modeling by using the AlphaFold2_multimer software, indicated that HMG20A forms a complex with PHF14 through the establishment of a two-stranded alpha-helical coiled-coil structure, Peer reviewed

Sample Processing Protocol Sample preparation Samples were dissolved in Urea 6M, 200mM ammonium bicarbonate, reduced with dithiothreitol (10 mM, 1 h, 37 °C) and alkylated in the dark with iodoacetamide (20 mM, 30 min, 25 °C). The protein mixture was then diluted 10 times with 200mM ammonium bicarbonate before being digested at 37 ºC overnight with trypsin (ration protein:enzyme 10:1). Peptides generated in the digestion were desalted with C18 column (Empore 3M, St. Paul, MN, USA), evaporated to dryness and resuspended in 0.1% formic acid. Chromatographic and mass spectrometric analysis Samples were analyzed using an LTQ-Orbitrap XL mass spectrometer (Thermo Fisher Scientific) coupled to an Agilent Technologies 1200 Series. Peptides were loaded onto C18 Zorbax precolumn (Agilent Technologies) and were separated by reversed-phase chromatography using a 12-cm column with an inner diameter of 75 μm, packed with 5 μm C18 particles (Nikkyo Technos Co.) using a 60 minute chromatographic gradients (3% to 35% acetonitrile, 0.1% formic acid). The mass spectrometer was operated in positive ionization mode with nanospray voltage set at 2.5 kV and source temperature at 200 °C. Ultramark 1621 for the FT mass analyzer was used for external calibration prior the analyses. Moreover, an internal calibration was also performed using the background polysiloxane ion signal at m/z 445.1200. The instrument was operated in data dependent acquisition (DDA) mode and full MS scans with 1 micro scans at resolution of 60.000 were used over a mass range of m/z 350-2000 with detection in the Orbitrap. Auto gain control (AGC) was set to 1E6, dynamic exclusion (60 seconds) and charge state filtering disqualifying singly charged peptides were activated. In each cycle of DDA analysis, following each survey scan the top ten most intense ions with multiple charged ions above a threshold ion count of 5000 were selected for fragmentation at normalized collision energy of 35%. Fragment ion spectra produced via collision-induced dissociation (CID) were acquired in the Ion Trap, AGC was set to 5e4 and isolation window to 2.0 m/z. All data were acquired with Xcalibur software. Data Processing Protocol Proteome Discoverer software suite (Thermo Fisher Scientific) and Mascot search engine Matrix Science) were used for peptide identification and quantitation. The data were searched against Swiss-Prot Human database. A precursor ion mass tolerance of 7 ppm at the MS1 level was used, and up to three miscleavages for trypsin were allowed. The fragment ion mass tolerance was set to 0.5 Da. Oxidation of methionine and N-terminal protein acetylation were used as variable modifications whereas carbamidomethylation on cysteines was set as a fixed modification, High mobility group proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A contains three well defined domains: an amino terminal intrinsically distorted domain, a high mobility group box with higher affinity for double stranded four-way-junction DNA than for lineal DNA and a long coiled-coil domain. Here we have found by a proteomic study that HMG20A copurify with the histone reader protein PHF14. Deletion analysis of the interaction domains and structural modeling by using AlphaFold2 software indicated that HMG20A forms a complex with PHF14 through the establishment of a two-stranded alpha-helical coiled-coil. Furthermore, PHF14 was essential for the stability and the chromatin localization of HMG20A. Transcriptomic analysis of triple negative human breast cancer cells demonstrated that PHF14 and HMG20A share a large subset of targets. PHF14 or HMG20A deficiency increased epithelial markers such as E-cadherin or p63 and components of the Hippo pathway and impaired mesenchymal phenotypes including cell migration, and invasion. Expression of mesenchymal adhesion molecules involved in metastasis such as L1CAM and LRRC15 were downregulated in PHF14 or HMG20A depleted cells in agreement with a decreased homotypic cell-cell adhesion ability. Inducible CRISPR inactivation of PHF14 or HMG20A genes impaired normal TGFβ-trigged epithelial to mesenchymal transition in mouse normal breast epithelial cells. Finally, we performed a meta-analysis of PHF14 and HMG20A genes in cancer databases. PHF14 gene is often amplified in different cancers which is associated to poor prognosis. In fact, high levels of PHF14 mRNA are associated to poor prognosis in many types of cancers. High expression of HMG20A and PHF14 are commonly associated to poor prognosis in sarcoma, colon and pancreas adenocarcinomas. In these tumors we found a clear correlation between the mRNA levels of both factors and also similar patterns of co-expressed genes with HMG20A and PHF14, indicating similar functions., Peer reviewed

Cumulative cultural evolution (CCE) occurs among humans who may be presented with many similar options from which to choose, as well as many social influences and diverse environments. It is unknown what general principles underlie the wide range of CCE dynamics and whether they can all be explained by the same unified paradigm. Here, we present a scalable evolutionary model of discrete choice with social learning, based on a few behavioural science assumptions. This paradigm connects the degree of transparency in social learning to the human tendency to imitate others. Computer simulations and quantitative analysis show the interaction of three primary factors—information transparency, popularity bias and population size—drives the pace of CCE. The model predicts a stable rate of evolutionary change for modest degrees of popularity bias. As popularity bias grows, the transition from gradual to punctuated change occurs, with maladaptive sub-populations arising on their own. When the popularity bias gets too severe, CCE stops. This provides a consistent framework for explaining the rich and complex adaptive dynamics taking place in the real-world, such as modern digital media., Peer reviewed

This is the database used in the script 'information_density_whitepapers'., Peer reviewed