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Simultaneous analysis of the intestinal parasites and diet through eDNA metabarcoding

Integrative Zoology 2023年第3期18卷 399-413页

作者： xabier cabodevilla Benjamín Juan GÓMEZ-MOLINER Naiara ABAD María JoséMADEIRA Department of Zoology and Animal Cell Biology Faculty of PharmacyUniversity of the Basque Country(UPV/EHU)AlavaSpain Instituto de Investigación en Recursos Cinegéticos(IREC)(CSIC-UCLM-JCCM) Ciudad RealSpain

Agricultural expansion and intensiﬁcation are having a huge impact on plant and arthropod diversity and abun-dance,affecting food availability for farmland birds.Difﬁcult food access,in turn,can lead to immunosuppression and a higher incidence of parasites.In the studies designed to examine changes in the diet of birds and their par-asites,metabarcoding is proving particularly useful.This technique requires mini-barcodes capable of amplifying the DNA of target organisms from fecal environmental DNA.To help to understand the impact of agricultural expansion on biodiversity,this study sought to design and identify mini-barcodes that might simultaneously as-sess diet and intestinal parasites from the feces of farmland birds.The capacity to identify diet and parasites of 2 existing and 3 newly developed mini-barcodes was tested“in silico”in relation to the behavior of a reference eukaryotic barcode.Among the newly designed mini-barcodes,MiniB18S_81 showed the higher taxonomic cover-age of eukaryotic taxa and a greater ampliﬁcation and identiﬁcation capacity for diet and parasite taxa.Moreover,when it was tested on fecal samples from 5 different steppe bird species,MiniB18S_81 showed high taxonomic resolution of the most relevant diet and parasite phyla,Arthropoda,Nematoda,Platyhelminthes,and Apicomplexa at the order level.Thus,the mini-barcode developed emerges as an excellent tool to simultaneously provide detailed information regarding the diet and parasites of birds,essential for conservation and management.

关键词： biomonitoring broad-spectrum primers eukaryotic mini-barcodes fecal eDNA farmland birds parasitology

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Multi-tissue transcriptomics of a unique monozygotic discordant twin case of severe progressive osseous heteroplasia

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Genes & Diseases 2024年第3期11卷 22-25页

作者： Alberto Gomez-Carballa Maria Jose Curras-Tuala Sara Pischedda Miriam Cebey-Lopez Jose Gomez-Rial Irene Rivero-Cale Jacobo Pardo-seco xabier Bello Sandra Viz-Lasheras Antonio Justicia-Grande Julian Montoto-Louzao Alba Camino-Mera Isabel Ferreiros-Vidal Maximo Fraga Jose RAntunez Rodolfo Gomez Federico Martinon-Torres Antonio Salas Genetics Vaccines and Infections Research Group(GENVIP)Instituto de Investigacion Sanitaria de SantiagoSantiagode CompostelaGalicia 15706Spain Translational Pediatrics and Infectious Diseases Department of PediatricsHospital Clinico Universitario de Santiago de CompostelaServicio Galego de Saude(SERGAS)Galicia 15706Spain Laboratorio de Inmunologia Servicio de Andlisis ClinicosHospital Clinico Universitario de Santiago de CompostelaServicio Galego de Saude(SERGAS)Galicia 15706Spain Unidade de Xenetica Instituto de Ciencias Forenses(INCIFOR)Facultade de MedicinaUniversidade de Santiago de Compostelaand GenPoB Research GroupInstituto de Investigacion SanitariaHospital Clinico Universitario de Santiago de CompostelaServicio Galego de Saude(SERGAS)Galicia 15706Spain Musculoskeletal Pathology Group Instituto de Investigacion Sanitaria de SantiagoServicio Galego de Saude(SERGAS)Santiago de CompostelaGalicia 15706Spain Department of Pathology Hospital Clinico Universitario de Santiago de Compostela(SERGAS)Galicia 15706Spain Unidad Integrada de BiobancosBiomodelos 3D y Modelos Animales IDIS(lnstituto de Investigacion Sanitaria de Santiagode Compostela)Galicia15706Spain Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias(CIBER-ES) MadridSpain

Progressive osseous heteroplasia(POH)is an ultra-rare autosomal dominant disabling disorder characterized by heterotopic ossification(HO).It is caused by heterozygous inactivating mutations in the GNAS(guanine nucleotide-binding protein alpha-stimulating activity polypeptide)gene.However,the molecular mechanisms underlying HO remain poorly understood.As a treatment for POH is not yet available,the identification of the mechanisms driving POH in affected tissues using gene expression may be of great help to underestand the molecular basis of POH and develop new therapeutic approaches.

关键词： stimulating driving asi

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Neoadjuvant immunotherapy in non-small-cell lung cancer:Times are changing—and fast

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World Journal of Clinical Oncology 2022年第9期13卷 758-761页

作者： Carlos Aguado Unai Jiménez Maestre xabier Mielgo-Rubio Department of Medical Oncology Hospital Universitario Clínico San CarlosMadrid 28040Spain Department of Thoracic Surgery Hospital Universitario CrucesBarakaldo 48903BizkaiaSpain Department of Medical Oncology Hospital Universitario Fundación AlcorcónAlcorcón 28922MadridSpain

Recent data from a phase 3 trial have shown that the addition of immunotherapy to neoadjuvant chemotherapy improves event-free survival in patients with nonsmall-cell lung cancer(NSCLC).This is the first positive phase 3 trial in this setting,although several phase 3 trials are currently investigating the efficacy of neoadjuvant and adjuvant immunotherapy in resectable NSCLC.

关键词： Neoadjuvant Immunotherapy NSCLC Perioperative Checkmate-816 nivolumab Chemo-immunotherapy

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Biliary spillage a new prognostic factor in gallbladder cancer?

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Hepatobiliary Surgery and Nutrition 2019年第5期8卷 537-538页

作者： xabier de Aretxabala Department of Surgery Clínica Alemana de SantiagoSantiagoChile

Gallbladder cancer is considered a rare disease associatedwith a dismal prognosis(1-3).However,since the irruptionof laparoscopic cholecystectomy,incidental cases haveincreased and prognosis improved.The main reason f... 详细信息

关键词： prognosis cancer gallbladder

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LIBRA:an adaptative integrative tool for paired single-cell multi-omics data

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Quantitative Biology 2023年第3期11卷 246-259页

作者： xabier Martinez-de-Morentin Sumeer AKhan Robert Lehmann Sisi Qu Alberto Maillo Narsis AKiani Felipe Prosper Jesper Tegner David Gomez-Cabrero Navarrabiomed Complejo Hospitalario de Navarra(CHN)Universidad Pública de Navarra(UPNA)IdiSNAPamplona 31001Spain Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and TechnologyThuwal 23955Saudi Arabia Algorithmic Dynamic Lab Department of Oncology and PathologyCenter for Molecular MedicineKarolinska InstituteStockholm 17177Sweden Division of Hemato-Oncology Center for Applied Medical Research CIMACancer Center University of Navarra(CCUN)Navarra Institute for Health Research(IDISNA)CIBERONCPamplona 31008Spain Department of Hematology Clinica Universidad de NavarraCIBERONC Pamplona 31008Spain Computer Electrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955Saudi Arabia

Background:Single-cell multi-omics technologies allow a profound system-level biology understanding of cells and tissues.However,an integrative and possibly systems-based analysis capturing the different modalities is challenging.In response,bioinformatics and machine learning methodologies are being developed for multi-omics single-cell analysis.It is unclear whether current tools can address the dual aspect of modality integration and prediction across modalities without requiring extensive parameter fine-tuning.Methods:We designed LIBRA,a neural network based framework,to learn translation between paired multi-omics profiles so that a shared latent space is constructed.Additionally,we implemented a variation,aLIBRA,that allows automatic fine-tuning by identifying parameter combinations that optimize both the integrative and predictive tasks.All model parameters and evaluation metrics are made available to users with minimal user iteration.Furthermore,aLIBRA allows experienced users to implement custom configurations.The LIBRA toolbox is freely available as R and Python libraries at GitHub(TranslationalBioinformaticsUnit/LIBRA).Results:LIBRA was evaluated in eight multi-omic single-cell data-sets,including three combinations of omics.We observed that LIBRA is a state-of-the-art tool when evaluating the ability to increase cell-type(clustering)resolution in the integrated latent space.Furthermore,when assessing the predictive power across data modalities,such as predictive chromatin accessibility from gene expression,LIBRA outperforms existing tools.As expected,adaptive parameter optimization(aLIBRA)significantly boosted the performance of learning predictive models from paired data-sets.Conclusion:LIBRA is a versatile tool that performs competitively in both“integration”and“prediction”tasks based on single-cell multi-omics data.LIBRA is a data-driven robust platform that includes an adaptive learning scheme.

关键词： single-cell multi-omic Autoencoder auto-finetuning

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Master of one trade:Arbutus unedo relies on plasticity to persist under habitats differing in water availability

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Journal of Plant Ecology 2017年第5期10卷 869-881页

作者： xabier Santiso Rubén Retuerto Área de Ecología Facultad de BiologíaCampus VidaUniversidade de Santiago de Compostela15782 Santiago de CompostelaSpain

Aims the limited water supply in the Mediterranean Basin will be exacerbated in the immediate future as result of severe drought events.thus,the study of the intraspecific variability in functional traits of plant species is important,because such variability modulates species’responses.Here,we aimed to analyse the variability in plasticity of physiological and structural traits of Arbutus unedo L.in response to water availability and to determine whether the levels of phenotypic plasticity varied in plants of different provenances.Methods We kept two sets of plants under contrasted water regimes(high water and low water)and calculated a phenotypic plasticity index to determine the plastic response to water stress.We compared the response among kind of traits and provenance.We also per-formed analysis of variance to assess the trait and provenance effect.Important Findings We found that biomass and key physiological traits decrease under drought conditions,while the water use efficiency increased.Plasticity differed between groups of traits,being higher in structural and gas exchange parameters,but the provenance did not account for signifi-cant variation in plasticity.A.unedo has evolved a‘good saver’strat-egy,involving decreasing growth and water use-when this resource is unavailable-together with the dissipation of excess of radiation that it cannot process.the homogeneous response between provenances may be the result of a canalization event.this strategy,based on a high degree of plasticity,is a probable determining factor in the success of the species over its wide range of environmental conditions and will be critical to withstand the ongoing environmental changes.

关键词： adaptation canalization contrasted provenances drought global change phenotypic plasticity

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Pitfalls of barcodes in the study of worldwide SARSCoV-2 variation and phylodynamics

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Zoological Research 2021年第1期42卷 87-93页

作者： Jacobo Pardo-Seco Alberto Gómez-Carballa xabier Bello Federico Martinón-Torres Antonio Salas Unidade de Xenética Instituto de Ciencias Forenses(INCIFOR)Facultade de MedicinaUniversidade de Santiago de Compostelaand GenPoB Research GroupInstituto de Investigación Sanitaria(IDIS)Hospital Clínico Universitario de Santiago(SERGAS)Galicia 15706Spain Genetics Vaccines and Pediatric Infectious Diseases Research Group(GENVIP)Instituto de Investigación Sanitaria de Santiago(IDIS)and Universidad de Santiago de Compostela(USC)Galicia 15706Spain Translational Pediatrics and Infectious Diseases Department of PediatricsHospital Clínico Universitario de Santiago de Compostela(SERGAS)Galicia 15706Spain

DEAR EDITOR,Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks.We show that purely mathematical procedures for site selection should be supervised by known phylogeny(i)to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties,and(ii)to avoid phylogenetic redundancy.We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites(as a proxy for phylogenetic-based criteria).This procedure demonstrates that,for short barcodes(e.g.,11 sites),there are thousands of informative site combinations that improve previous proposals.We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny,such that most representative genomes in these ancestral nodes are no longer in circulation.Consequently,coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.

关键词： dynamics properly purely

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Biogeographical informativeness of Y-STR haplotypes

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Science Bulletin 2019年第19期64卷 1381-1384页

作者： Jacobo Pardo-Seco Alberto Gómez-Carballa xabier Bello Federico Martinón-Torres Antonio Salas Unidade de Xenética Instituto de Ciencias Forenses(INCIFOR)Facultade de MedicinaUniversidade de Santiago de Compostelaand GenPoB Research GroupInstitutode Investigaciones Sanitarias(IDIS)Hospital Clínico Universitario de Santiago(SERGAS)GaliciaSpain Grupo de Investigación en Genética VacunasInfecciones y Pediatría(GENVIP)Universidade de Santiago de Compostelaand Hospital Clínico Universitario de Santiago(SERGAS)GaliciaSpain

Research on biogeographical ancestry(BGA)is becoming of growing interest in forensic genetics and in the biomedical literature(1)Thus,for instance,the need to predict ethnicity of an unknown suspect based on DNA profiles found at the crime scene is of maximum interest in criminalistics[2],and several autosomal SNP panels have been designed and tested for BGA investigations[3,4].Most of these panels aim at discriminating three main continental groups(sub-Saharan Africans,Europeans,and Asians)by way of testing a number of ancestry informative markers(AIMs)that run from a few dozens to a few hundred[5](see more background in Supplementary data online).

关键词： BGA STR Biogeographical informativeness of Y-STR haplotypes

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Electro-tribological properties of diamond like carbon coatings

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Friction 2020年第2期8卷 451-461页

作者： Iñigo BRACERAS Iñigo IBÁNEZ Santiago DOMINGUEZ-MEISTER xabier VELASCO Marta BRIZUELA Iñaki GARMENDIA Tecnalia Research&Innovation Mikeletegi Pasealekua 2Donostia-San Sebastian 20009Spain Mechanical Engineering Department University of the Basque Country UPV/EHUPlaza de Europa1Donostia-San Sebastian 20018Spain

Diamond like carbon(DLC)coatings typically present good self-lubricating tribological properties that could be of interest in sliding dielectric contacts in multiple electrical applications.In this work electro-tribological studies have been performed on several DLC coatings against aluminum in different humidity conditions,in which the coefficients of friction(CoFs)and electrical contact resistance(ECR)were continuously monitored.Results show that CoF and ECR data can be linked to the properties of the coatings(thickness,finishing,microstructure,residual stresses,and wettability)and the degradation modes of their tribological and electrical properties.Therefore,electro-tribological data can provide valuable information about the performance of dielectric coatings,the reasons behind it,and assist in the development of the coatings.ECR also shows potential for on-line monitoring of coated parts in operation.

关键词： DLC electro-tribology ECR-electrical contact resistance coefficient of friction

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Phylogeography of SARS-CoV-2 pandemic in Spain:a story of multiple introductions,micro-geographic stratification,founder effects,and super-spreaders

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Zoological Research 2020年第6期41卷 605-620页

作者： Alberto Gomez-Carballa xabier Bello Jacobo Pardo-Seco Maria Luisa Perez del Molino Federico Martinon-Torres Antonio Salas Unidade de Xendtica Instituto de Ciencias Forenses(I NCI FOR)Facultade de MedicinaUniversidade de Santiago de Compostelaand GenPoB Research GroupInstituto de Investigaci6n Sanitaria(IDIS)Hospital Clinico Universitario de Santiago(SERGAS)Galicia 15706Spain Genetics Vaccines and Pediatric Infectious Diseases Research Group(GENVIP)Instituto de Investigacion Sanitaria de Santiago(IDIS)and Universidade de Santiago de Compostela(USC)Galicia 15706Spain Translational Pediatrics and Infectious Diseases Department of PediatricsHospital Clinico Universitario de Santiago de Compostela(SERGAS)Galicia 15706Spain Servicio de Microbiologia y Parasitologia Complejo Hospitalario Universitario de Santiago de CompostelaSantiago de CompostelaGalicia15706 Spain

Spain has been one of the main global pandemic epicenters for coronavirus disease 2019(COVID-19).Here,we analyzed>41000 genomes(including>26000 high-quality(HQ)genomes)downloaded from the GISAID repository,including 1245(922 HQ)sampled in Spain.The aim of this study was to investigate genome variation of novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and reconstruct phylogeographic and transmission patterns in Spain.Phylogeographic analysis suggested at least 34 independent introductions of SARS-CoV-2 to Spain at the beginning of the outbreak.Six lineages spread very successfully in the country,probably favored by super-spreaders,namely,A2 a4(7.8%),A2 a5(38.4%),A2 a10(2.8%),B3 a(30.1%),and B9(8.7%),which accounted for 87.9% of all genomes in the Spanish database.One distinct feature of the Spanish SARS-Cov-2 genomes was the higher frequency of B lineages(39.3%,mainly B3 a+B9)than found in any other European country.While B3 a,B9,(and an important sub-lineage of A2 a5,namely,A2 a5 c)most likely originated in Spain,the other three haplogroups were imported from other European locations.The B3 a strain may have originated in the Basque Country from a B3 ancestor of uncertain geographic origin,whereas B9 likely emerged in Madrid.The time of the most recent common ancestor(TMRCA)of SARS-CoV-2 suggested that the first coronavirus entered the country around 11 February 2020,as estimated from the TMRCA of B3 a,the first lineage detected in the country.Moreover,earlier claims that the D614 G mutation is associated to higher transmissibility is not consistent with the very high prevalence of COVID-19 in Spain when compared to other countries with lower disease incidence but much higher frequency of this mutation(56.4% in Spain vs.82.4% in rest of Europe).Instead,the data support a major role of genetic drift in modeling the micro-geographic stratification of virus strains across the country as well as the role of SARS-CoV-2 super-spreaders.

关键词： Covid-19 SARS-CoV-2 Genomics Phylogeny Phylogeography

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