On the holobiont 'predictome' of immunocompetence in pigs

Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default. The online version contains supplementary material available at 10.1186/s12711-023-00803-4

Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes

The role of somatic mutations in complex diseases, including neurodevelopmental and neurodegenerative disorders, is becoming increasingly clear. However, to date, no study has shown their relation to Parkinson disease's phenotype. To explore the relevance of embryonic somatic mutations in sporadic Parkinson disease, we performed whole-exome sequencing in blood and four brain regions of ten patients. We identified 59 candidate somatic single nucleotide variants (sSNVs) through sensitive calling and a careful filtering strategy (COSMOS). We validated 27 of them with amplicon-based ultra-deep sequencing, with a 70% validation rate for the highest-confidence variants. The identified sSNVs are in genes with synaptic functions that are co-expressed with genes previously associated with Parkinson disease. Most of the sSNVs were only called in blood but were also found in the brain tissues with ultra-deep amplicon sequencing, demonstrating the strength of multi-tissue sampling designs

Diagnostic and Prognostic Value of Cardiac Imaging in Amyloidosis

[Abstract] Amyloidosis is an infiltrative disease caused by extracellular protein deposition that has accumulated a lot of scientific production in recent years. Different types of amyloidosis can affect the heart. Transthyretin amyloidosis and light chain amyloidosis are the two most common types of cardiac amyloidosis. These entities have a poor prognosis, so accurate diagnostic techniques are imperative for determining an early therapeutic approach. Recent advances in cardiac imaging and diagnostic strategies show that these tools are safe and can avoid the use of invasive diagnostic techniques to histological confirmation, such as endomyocardial biopsy. We performed a review on the diagnostic and prognostic implications of different cardiac imaging techniques in cardiac amyloidosis. We mainly focus on reviewing echocardiography, cardiac magnetic resonance, computed tomography and nuclear imaging techniques and the different safety measurements that can be done with each of them

The sodium transporter encoded by the HKT1;2 gene modulates sodium/potassium homeostasis in tomato shoots under salinity

[EN] Excessive soil salinity diminishes crop yield and quality. In a previous study in tomato, we identified two closely linked genes encoding HKT1-like transporters, HKT1;1 and HKT1;2, as candidate genes for a major quantitative trait locus (kc7.1) related to shoot Na+/K+ homeostasis - a major salt tolerance trait - using two populations of recombinant inbred lines (RILs). Here, we determine the effectiveness of these genes in conferring improved salt tolerance by using two near-isogenic lines (NILs) that were homozygous for either the Solanum lycopersicum allele (NIL17) or for the Solanum cheesmaniae allele (NIL14) at both HKT1 loci; transgenic lines derived from these NILs in which each HKT1;1 and HKT1;2 had been silenced by stable transformation were also used. Silencing of ScHKT1;2 and SlHKT1;2 altered the leaf Na+/K+ ratio and caused hypersensitivity to salinity in plants cultivated under transpiring conditions, whereas silencing SlHKT1;1/ScHKT1;1 had a lesser effect. These results indicate that HKT1;2 has the more significant role in Na+ homeostasis and salinity tolerance in tomato.We thank Dr Espen Granum for critically reading the manuscript, Maria Isabel Gaspar Vidal and Elena Sanchez Romero for technical assistance, the Instrumental Technical Service at EEZ-CSIC for DNA sequencing and ICP-OES mineral analysis and Michael O'Shea for proofreading the text. In addition, we thank Dr Ana P. Ortega who assisted in preliminary experiments. This work was supported by ERDF-cofinanced grants, AGL2010-17090 and AGL2013-41733-R (A.B.), AGL2015-64991-C3-3-R (V.M.) and AGL2014-56675-R (M.J.A.) from the Spanish "Ministerio de Economia, Industria y Competitividad'; CVI-7558, Proyecto de Excelencia, from Junta de Andalucia (A.B); and the Australian Research Council (ARC) for Centre of Excellence (CE14010008) and Future Fellowship (FT130100709) funding (M.G.). N.J-P. was supported by an FPI program BES-2011-046096 and her stay in M.G.'s lab by a short-stay EEBB-I-14-08682, both from the Spanish from "Ministerio de Economia Industria y Competitividad'. The authors have no conflict of interest to declare.Jaime-Perez, N.; Pineda Chaza, BJ.; García Sogo, B.; Atarés Huerta, A.; Athman, A.; Byrt, CS.; Olias, R.... (2017). The sodium transporter encoded by the HKT1;2 gene modulates sodium/potassium homeostasis in tomato shoots under salinity. Plant Cell & Environment. 40(5):658-671. https://doi.org/10.1111/pce.12883S65867140

Transition path to a dense efficient-packed post-delafossite phase. Crystal structure and evolution of the chemical bonding

[EN] A(I)B(III)O(2) delafossite-type oxides are important technological compounds characterized by the linear coordination of the monovalent A metal by oxygen atoms. Based on results of in situ synchrotron X-ray diffraction measurements and ab initio calculations, we herein report on the high-pressure behavior of AgGaO2, to the best of our knowledge the first compound showing step-wise transitions of Ag coordination from linear (2) to octahedral (6), through a leaning delafossite structure. These transformations take place at similar to 10.5 and similar to 16.5 GPa, respectively. Our structural analysis evidences that the initial rhombohedral delafossite structure first becomes dynamically unstable, and distorts continuously via a gliding motion of the [GaO2] octahedral layers within the ab plane, and subsequently transform into another rhombohedral phase 8% denser. This structural sequence is associated with a simultaneous decrease in the bond order of the Ag-O bonds and an increase in the ionicity of the crystal. These results may help to unveil the high-pressure phases of several delafossite compounds which were reported to undergo phase transitions under compression that could not be identified.We are thankful for the financial support received from the Spanish Ministerio de Ciencia e Innovacion and the Agencia Estatal de Investigacion under national projects PGC2018-094417-B-I00 (co-financed by EU FEDER funds), MAT2016-75586-C4-1-P/2-P, FIS2017-83295-P, PID2019-106383GB-C41/C42 and RED2018-102612-T (MALTA Consolider), and from Generalitat Valenciana under project PROMETEO/2018/123. D.S-P, A.O.R, and J.A.S acknowledge financial support of the Spanish MINECO for the RyC-2014-15643, RyC-2016-20301, and RyC-2015-17482 Ramon y Cajal Grants, respectively. Authors thank ALBA-CELLS synchrotron for providing beamtime (ALBA experiments 2012010170).Chuliá-Jordán, R.; Santamaria-Perez, D.; Pellicer-Porres, J.; Otero-De-La-Roza, A.; Martinez-Garcia, D.; García-Domene, B.; Gomis, O.... (2021). Transition path to a dense efficient-packed post-delafossite phase. Crystal structure and evolution of the chemical bonding. Journal of Alloys and Compounds. 867. https://doi.org/10.1016/j.jallcom.2021.15901215901286

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates

Reproductive fluids, added to the culture media, contribute to minimizing phenotypical differences between in vitro-derived and artificial insemination-derived piglets

The addition of reproductive fluids (RF) to the culture media has shown benefits in different embryonic traits but its long-term effects on the offspring phenotype are still unknown. We aimed to describe such effects in pigs. Blood samples and growth parameters were collected from piglets derived from in vitro-produced embryos (IVP) with or without RF added in the culture media versus those artificially inseminated (AI), from day 0 to month 6 of life. An oral glucose tolerance test was performed on day 45 of life. We show here the first comparative data of the growth of animals produced through different assisted reproductive techniques, demonstrating differences between groups. Overall, there was a tendency to have a larger size at birth and faster growth in animals derived from in vitro fertilization and embryo culture versus AI, although this trend was diminished by the addition of RFs to the culture media. Similarly, small differences in hematological indices and glucose tolerance between animals derived from AI and those derived from IVP, with a sex-dependent effect, tended to fade in the presence of RF. The addition of RF to the culture media could contribute to minimizing the phenotypical differences between the in vitro-derived and AI offspring, particularly in males

EpiGe: A machine-learning strategy for rapid classification of medulloblastoma using PCR-based methyl-genotyping

Molecular classification of medulloblastoma is critical for the treatment of this brain tumor. Array-based DNA methylation profiling has emerged as a powerful approach for brain tumor classification. However, this technology is currently not widely available. We present a machine-learning decision support system (DSS) that enables the classification of the principal molecular groups—WNT, SHH, and non-WNT/non-SHH—directly from quantitative PCR (qPCR) data. We propose a framework where the developed DSS appears as a user-friendly web-application—EpiGe-App—that enables automated interpretation of qPCR methylation data and subsequent molecular group prediction. The basis of our classification strategy is a previously validated six-cytosine signature with subgroup-specific methylation profiles. This reduced set of markers enabled us to develop a methyl-genotyping assay capable of determining the methylation status of cytosines using qPCR instruments. This study provides a comprehensive approach for rapid classification of clinically relevant medulloblastoma groups, using readily accessible equipment and an easy-to-use web-application.The study was supported by Associations of Parents and Families of Children with Cancer and by funding of the Spanish Ministry of for Science, Innovation and University (grant PI20/00519; PI CL) and the Foundation La Marató TV3 (grant 201921-30; PI CL). We acknowledge the multidisciplinary team who helped in the molecular analyses and care of patients, and the BioBank Hospital Sant Joan de Déu of the Spanish BioBank Network for sample procurement. We also acknowledge Marta Fortuny for communication strategy advice and Eduard Puig for legal assistance and data protection regulations. Authors acknowledge the SJD Fundraising Team.Peer ReviewedArticle signat per 23 autors/es: Soledad Gómez-González, Joshua Llano, Marta Garcia, Alicia Garrido-Garcia, Mariona Suñol, Isadora Lemos, Sara Perez-Jaume, Noelia Salvador, Nagore Gene-Olaciregui, Raquel Arnau Galán, Vicente Santa-María, Marta Perez-Somarriba, Alicia Castañeda, José Hinojosa, Ursula Winter, Francisco Barbosa Moreira, Fabiana Lubieniecki, Valeria Vazquez, Jaume Mora, Ofelia Cruz, Andrés Morales La Madrid, Alexandre Perera, Cinzia Lavarino.Postprint (published version

Creación de página Web para promover aprendizaje colaborativo en alumnos de máster

[EN] A Web page has been designed by master students in order to engage them in collaborative and cooperative learning, thus improving their learning and comprehension of relevant concepts and topics. To that purpose, topics included in the subject Advanced Techniques in Chemistry which is part of the Master in Sustainable Chemistry of the University of Valencia have been included in the Webpage with the help of WIX software. This approach makes intensive use of the Web as a key technological resource for learning, where the information seen in the subject is summarized and given in an applicative and pertinent context that is easy to understand for all public interested in the topics discussed in there. This tool allows the development of a key digital competence in the Spanish educational system, articulating the development of the Website with the management of multimedia content. It also allows a sense of initiative and entrepreneurship, since it is of total freedom on the part of the students working in group, the uploaded content, always following the knowledge developed and acquired in the subject.[ES] Se ha diseñado una página web para involucrar a los estudiantes de máster en el aprendizaje colaborativo y cooperativo, mejorando así su aprendizaje y comprensión de los temas y conceptos relevantes. Para ello, los temas incluidos en la asignatura Técnicas Avanzadas en Química que forma parte del Máster en Química Sostenible de la Universidad de Valencia se han incluido en la página web con la ayuda del software WIX. Este enfoque hace un uso intensivo de la web como recurso tecnológico clave de aprendizaje, donde se resume la información vista en la asignatura y se le da un contexto aplicativo y pertinente fácil de entender para todo el público interesado en los temas allí tratados. Esta herramienta permite el desarrollo de una competencia digital clave en el sistema educativo español, articulando el desarrollo de la página web con el manejo de contenido multimedia. Además permite un sentido de iniciativa y emprendimiento, ya que hay libertad por parte de los estudiantes trabajando en grupo, para sellecionar el contenido de la página, siempre siguiendo el conocimiento desarrollado y adquirido en la asignatura y el asesoramiento de la profesora.González Béjar, M.; Cuaran Acosta, D.; Andrés Olmos, L.; Rosa Pardo, I.; Del Rincón, R.; Zaballos García, E.; Perez Prieto, J. (2018). Creación de página Web para promover aprendizaje colaborativo en alumnos de máster. En IN-RED 2018. IV Congreso Nacional de Innovación Educativa y Docencia en Red. Editorial Universitat Politècnica de València. 348-355. https://doi.org/10.4995/INRED2018.2018.8756OCS34835

Exploiting the potential of autophagy in cisplatin therapy: a new strategy to overcome resistance

Resistance to cisplatin is a major challenge in the current cancer therapy. In order to explore new therapeutic strategies to cisplatin resistance, we evaluated, in a model of lung cancer (H1299 and H460 cell lines), the nature of the pathways leading to cell death. We observed that H1299 displayed a natural resistance to cisplatin due to an inability to trigger an apoptotic response that correlates with the induction of autophagy. However, pharmacological and genetic approaches showed how autophagy was a mechanism associated to cell death rather than to resistance. Indeed, pro-autophagic stimuli such as mTOR or Akt inhibition mediate cell death in both cell lines to a similar extent. We next evaluated the response to a novel platinum compound, monoplatin, able to promote cell death in an exclusive autophagy-dependent manner. In this case, no differences were observed between both cell lines. Furthermore, in response to monoplatin, two molecular hallmarks of cisplatin response (p53 and MAPKs) were not implicated, indicating the ability of this pro-autophagic compound to overcome cisplatin resistance. In summary, our data highlight how induction of autophagy could be used in cisplatin resistant tumours and an alternative treatment for p53 mutated patient in a synthetic lethally approach