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Gintegrator: Enhancing biological sequences data integration with real-time identifier translation
No full textAdvancements in genomic and proteomic sequencing, along with molecular biology techniques, have led to the generation of vast amounts of sequence data stored in different collaborative databases. The integration of these heterogeneous data sources holds immense potential for advancing our understanding of biological systems and processes, although it presents several challenges due to inconsistencies in formats and annotations. To address this, we introduce Gintegrator, a web application that streamlines the process of translating gene and protein identifiers across major sequence databases such as NCBI, UniProt and KEGG. By introducing the use of identical or similar genes and proteins in the translation workflow, and performing real-time queries to access the most recent data, Gintegrator enhances both the accuracy and success rate of identifier mapping, while also facilitating efficient and reliable biological data integration and analysis for researchers.This work was supported by the Spanish Ministry of Science and Innovation [PID2022-139798OB-I00], the Spanish Ministry of Science and Innovation (Health Institute Carlos III) [PI23/01522], and the Spanish Ministry of Universities [FPU22/00336].Peer reviewe
Intestinal compartmentalization of antigen-specific Treg cells following oral allergen exposure in mice
No full textPóster presentado al Immunology Winter School, celebrado en Schladming, Austria del 30 de enero al 2 de febrero de 2025.N
Documentación do castro de A Roda con LiDAR aéreo e magnetometría
No full textO obxectivo principal da intervención consistiu en documentar estruturas arqueolóxicas asociadas ao castro de A Roda (Pobra do Brollón, Lugo). Estas estruturas, en función do seu estado, pódense dividir en dous: As primeiras correspóndense a aquelas que, aínda que permanecen enterradas, son visibles indirectamente pola alteración topográfica que producen. Ditas estruturas son murallas, parte dos seus fosos e outras alteracións singulares. Para detectar e documentar este tipo de elementos utilizouse o LiDAR aéreo. As segundas estruturas correspóndense a aquelas que ademais de estar enterradas non se reflicten nin directa nin indirectamente a través de ningún sinal visible na superficie, e por tanto non son detectables a partir da topografía ou a vexetación. Devanditos elementos son construcións como muros de cabanas ou outros elementos como fogares, accesos ou camiños. Para detectar e documentar este tipo de estruturas utilizouse a prospección xeomagnética.
O obxectivo secundario da intervención foi documentar a estrutura actual da paisaxe e todos os elementos que constitúen a contorna do sitio. Os produtos obtidos como a Ortoimaxen e os Modelos Dixitais do Terreo (MDT) permiten caracterizar os camiños, os usos do chan, o parcelario, etc. Algúns destes elementos sérvennos para entender a evolución da paisaxe ao longo do tempo.Comunidade de Montes Salcedo e BeranN
Advancing personalized medicine in Alzheimer’s disease: Liquid biopsy epigenomics unveil APOE ε4-linked methylation signatures
No full textThis article belongs to the Special Issue Advances in Aging and Alzheimer’s Disease Research: From Molecular Mechanisms to Therapeutics.Recent studies show that patients with Alzheimer’s disease (AD) harbor specific methylation marks in the brain that, if accessible, could be used as epigenetic biomarkers. Liquid biopsy enables the study of circulating cell-free DNA (cfDNA) fragments originated from dead cells, including neurons affected by neurodegenerative processes. Here, we isolated and epigenetically characterized plasma cfDNA from 35 patients with AD and 35 cognitively healthy controls by using the Infinium® MethylationEPIC BeadChip array. Bioinformatics analysis was performed to identify differential methylation positions (DMPs) and regions (DMRs), including APOE ε4 genotype stratified analysis. Plasma pTau181 (Simoa) and cerebrospinal fluid (CSF) core biomarkers (Fujirebio) were also measured and correlated with differential methylation marks. Validation was performed with bisulfite pyrosequencing and bisulfite cloning sequencing. Epigenome-wide cfDNA analysis identified 102 DMPs associated with AD status. Most DMPs correlated with clinical cognitive and functional tests including 60% for Mini-Mental State Examination (MMSE) and 80% for Global Deterioration Scale (GDS), and with AD blood and CSF biomarkers. In silico functional analysis connected 30 DMPs to neurological processes, identifying key regulators such as SPTBN4 and APOE genes. Several DMRs were annotated to genes previously reported to harbor epigenetic brain changes in AD (HKR1, ZNF154, HOXA5, TRIM40, ATG16L2, ADAMST2) and were linked to APOE ε4 genotypes. Notably, a DMR in the HKR1 gene, previously shown to be hypermethylated in the AD hippocampus, was validated in cfDNA from an orthogonal perspective. These results support the feasibility of studying cfDNA to identify potential epigenetic biomarkers in AD. Thus, liquid biopsy could improve non-invasive AD diagnosis and aid personalized medicine by detecting epigenetic brain markers in blood.The authors sincerely appreciate the funding support from the Government of Navarra [GºNa 36/18], and the Spanish Government through grants from the Institute of Health Carlos III (FIS PI20/01701), co-funded by the European Regional Development Fund (ERDF), European Union, A way of shaping Europe. The project leading to these results has received funding from La Caixa Banking Foundation (ID 100010434) and Fundación Luzón (HR20 01109_BIOP ALS) under agreement LCF/PR/PR15/51100006. In addition, M.M. (Mónica Macías) is beneficiary of a Río Hortega grant from the Spanish Government (CM20/00240) and a Navarrabiomed postdoctoral research grant (2022). B.A. (Blanca Acha) is supported by a PFIS fellowship from the Spanish Government (FI18/00150). J.Á.-J. (Johana Álvarez-Jiménez) has received a Doctorandos industriales grant for 2023–2026. A.U.-C. (Amaya Urdánoz-Casado) received a Doctorandos industriales grant for 2018–2020 and a predoctoral research grant (2019) founded by the Department of Industry and Health of the Government of Navarra. D.A. was supported by research grants from the Institute of Health Carlos III (ISCIII), Spain INT19/00016 and INT23/00048. M.M. (Maite Mendioroz) received a Contrato de intensificación grant from the Institute of Health Carlos III (INT19/00029) and a grant (LCF/PR/PR15/51100006) founded by La Caixa Banking Foundation and Caja Navarra Banking Foundation.Peer reviewe
The Gaia-ESO survey: A quiescent milky way with no significant dark/stellar accreted disc
No full textAccording to our current cosmological model, galaxies like the Milky Way are expected to experience many mergers over their lifetimes. The most massive of the merging galaxies will be dragged towards the disc plane, depositing stars and dark matter into an accreted disc structure. In this work, we utilize the chemodynamical template developed in Ruchti et al. to hunt for accreted stars. We apply the template to a sample of 4675 stars in the third internal data release from the Gaia-ESO Spectroscopic Survey. We find a significant component of accreted halo stars, but find no evidence of an accreted disc component. This suggests that the Milky Way has had a rather quiescent merger history since its disc formed some 8-10 billion years ago and therefore possesses no significant dark matter disc. © 2015 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.GRR, SF, and TB acknowledge support from the project grant ‘The New Milky Way’ from the Knut and Alice Wallenberg Foundation. JIR would like to acknowledge support from SNF grant PP00P2_128540/1. This work was partially supported by grants ESP2013-41268-R (MINECO) and 2014SGR-1458 (Generalitat of Catalunya). KL acknowledges support from the European Union FP7-PEOPLE-2012-IEF grant no. 328098. UH acknowledges support from the Swedish National Space Board (SNSB/Rymdstyrelsen). LS acknowledges the support of Chile's Ministry of Economy, Development, and Tourism's Millennium Science Initiative through grant IC120009, awarded to The Millennium Institute of Astrophysics, MAS. This work was partly supported by the European Union FP7 programme through ERC grant number 320360 and by the Leverhulme Trust through grant RPG-2012-541. We acknowledge the support from INAF and Ministero dell’ Istruzione, dell’ Università’ e della Ricerca (MIUR) in the form of the grant ‘Premiale VLT 2012’. The results presented here benefit from discussions held during the Gaia-ESO workshops and conferences supported by the ESF (European Science Foundation) through the GREAT Research Network Programme
Comparative analysis of gut microbiome-derived short-chain fatty acids in patients with severe mental disorder: Insights from schizophrenia and bipolar disorder
No full textBoth schizophrenia (SZ) and bipolar disorder (BD) are associated with disruptions in the gut microbiome. Short-chain fatty acids (SCFAs), such as acetate, propionate and butyrate, are key metabolites produced by gut bacteria that influence brain function, immune responses and behaviour. We conducted a cross-sectional observational study with 123 patients (86 with SZ and 37 with BD). We analysed faecal samples for SCFA and examined associations with clinical (psychopathology and cognition), metabolic and lifestyle factors. We performed analysis of covariance to find differences in SCFA levels between diagnostic groups, adjusting for covariates. Faecal SCFA levels were numerically higher in the SZ group than in the BD group. However, after adjusting for covariates, a significant sex-by-diagnosis interaction was observed only for acetate levels. Body mass index emerged as a key predictor of SCFA levels but we observed no significant associations with other metabolic or lifestyle variables, including diet, physical activity and blood inflammatory biomarkers. Additionally, SCFA levels showed no correlation with symptom severity or cognitive performance in either group. This study is the first to compare SCFA profiles between SZ and BD, highlighting potential differences in gut microbiota-derived metabolites between these disorders. These findings suggest greater disruption of the gut-brain axis in SZ, potentially reflecting distinct pathophysiological mechanisms involving metabolic and sex-related factors. Further research, including blood SCFA measurements, could better explain the role of SCFAs and explore microbiota-targeted therapeutic strategies for SZ and BD.This study was partly supported by a grant from the Foundation for Research and Biosanitary Innovation in the Principality of Asturias (FINBA) “Convocatoria Intramural para el Fomento de Proyectos de Investigación entre Investigadores Nóveles - Ref. GOBLL/ 2021-051-INTRAMURAL NOV-GOBLL”, sponsored by Janssen; by a grant from the Ministry of Economy and Competitiveness the Instituto de Salud Carlos III (ISCIII, grant number PI21/01393) and co-funded by the European Union, CIBER – Consorcio Centro de Investigación Biomédica en Red - (CB/07/09/0020); and by the Government of the Principality of Asturias ref. IDE/2024/774. The funders played no further role in study design, in collection, analysis, and interpretation of data, or in writing the report or the decision to submit the paper for publication.Peer reviewe
Additional file 1 of Mating from a female perspective: Do brown bear females play an active role in mate searching?
No full textMCIN/AEI/ 10.13039/501100011033 European Regional Development Fund LIFE17NAT/IT/464 SAFE-CROSSING Romanian National Authority for Scientific Research and Innovation Creșterea capacității și performanței instituționale a INCDS ‘Marin Drăcea’ în activitatea de CDI—CresPerfInst Joachim and Hanna Schmidt Stiftung für Umwelt und Verkehr, Germany European Union-NextGenerationEU, Ministerio de Universidades y Plan de Recuperacion, Transformacion y Resiliencia Consejo Superior de Investigaciones Cientificas (CSIC)Peer reviewe
Supplemental Material: Symmetry origin and microscopic mechanism of electrical magnetochiral anisotropy in tellurium
No full textSupplementary Section 1. Methods.Supplementary Section 2. First-order electronic transport of Tellurium.Supplementary Section 3. Second-order electronic transport of Tellurium.Supplementary Section 4. How a combination of non-linear conductivity and ordinary Hall can give a contribution that mimics eMChA.Supplementary Section 5. Scaling law of eMChA.Peer reviewe
The Effects of Marine Redox Variability on Magnetic Mineralogy: An Environmental Magnetic Study of late Miocene Sediments from IODP Expedition 401, Site U1385
No full textPóster presentado en AGU Fall Meeting (2024), 9-13th december in Washington, D.C.
IODP Expeditions 401 ScientistsThe southwestern Iberian continental margin has long been recognized as a valuable paleoclimate record due to its preservation of millennial-scale climate signals. Large sedimentation rates (~20 cm/ka) allow for high-fidelity preservation of high-resolution climate variability, and have yielded rock-magnetic insight into the regional and global contributions of eolian iron-oxides from the Sahara, magnetic fabrics as a proxy for decoding the Mediterranean Outflow Water (MOW) variability, and the paleoclimatic potential of magnetofossils. This study examines the magnetic properties of the late Miocene-aged cores collected from site U1385 by International Ocean Discovery Program (IODP) Expedition 401. Measurements include in-line core scanning of geophysical properties for magnetic susceptibility (MS); natural gamma radiation (NGR) and X-ray fluorescence. Additionally, detailed rock magnetic experiments at room- (hysteresis, IRM acquisition, FORCs) and low-temperature magnetometry were conducted to characterize the magnetic mineralogy. Preliminary results show that cyclical patterns in magnetic susceptibility are controlled primarily by varying concentrations of fine-grained ferrimagnetic magnetite and paramagnetic siderite. Furthermore, low-temperature magnetometry reveals an anomalous zone potentially enriched in goethite, which corresponds with elevated values of elemental ratios associated with redox changes (Mn/Fe, Mn/Ti, Mn/Al), as well as a temporary antiparallel relationship between the MS and NGR values. Although a terrigenous source for the goethite cannot be ruled out, the lack of observable hematite and the geochemical redox proxies imply that the goethite is likely a result of redox variability. The cause of these redox changes remains an area of active research, but caution should be exercised when using magnetic-records to reconstruct paleoclimate from this region
Temporal and cross-sectional associations of serum per- and polyfluoroalkyl substances (PFAS) and lipids from 1986 to 2016 - The Tromsø study
No full textPer- and polyfluoroalkyl substances (PFAS) have been linked to effects on human lipid profiles, with several epidemiological studies reporting associations between specific PFAS and blood lipid concentrations. However, these associations have been inconsistent, and most studies have focused on cross-sectional analyses with limited repeated measurements.The analyses for lipids and PFAS were funded by the Northern Norway Regional Health Authority through project No HNF147-19 and SFP1289-16, the Department of Laboratory Medicine, UNN, and The Tromsø Study, UiT. The funders had no influence on the design of the study. The PhD project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant, agreement No 860665 PERFORCE3.Peer reviewe