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Effect of primary structural variation on cervid prion protein in flexibility, stability, and spontaneous misfolding propensity
Get PDFProtein misfolding is central to numerous neurodegenerative disorders, collectively known as proteinopathies, which include Alzheimer's disease, Parkinson's disease, and prion diseases, among others. In many cases, specific polymorphisms of the proteins associated with these diseases influence their misfolding. However, the precise ways in which these polymorphisms affect protein integrity and how they contribute to misfolding propensity remain unclear. In the case of prion diseases, they are caused by prions or PrPSc, the misfolded isoforms of the cellular prion protein (PrPC). Chronic Wasting Disease (CWD) is a prion disease that affects cervids and can exhibit lymphotropic properties, making it the most widespread proteinopathy. For that reason, cervid PrPs and their polymorphisms have been extensively studied. To better understand the role of these polymorphisms, we analyzed 45 cervid PrP variants to assess their effects on flexibility, stability, and spontaneous misfolding propensity.
The cervid variants were expressed as recombinant PrP in E. coli and were analyzed for thermal stability using circular dichroism. Additionally, the rec-PrPs served as substrates for Protein Misfolding Shaking Amplification (PMSA), enabling assessment of each variant's spontaneous misfolding propensity. This process led to the formation of bona fide prions, as confirmed by inoculation of one of the resulting conformers into transgenic mice expressing bank vole PrP. In parallel, molecular dynamics simulations were conducted to analyze the structural flexibility of the variants. While differences in protein flexibility were observed, no correlation was detected among flexibility, thermal stability, and the observed variable spontaneous misfolding propensity, suggesting that these properties are independent parameters.The present work was partially funded by three different grants awarded by “Agencia Estatal de Investigación, Ministerio de Ciencia e Innovación” (Spanish Government), grant numbers PID2021-122201OB-C21, PID2021-1222010B-C22, and PID2020-117465GB-I00, funded by MCIN/AEI /10.13039/501100011033 and co-financed by the European Regional Development Fund (ERDF). Also funded by MCIN/AEI /10.13039/501100011033, F.P. and G.J.O. were provided with the grants RYC2022-036457-I and PID2021-125946OB-I00, respectively. EFA031/01 NEURO-COOP, which is co-funded at 65 % by the European Union through Programa Interreg VI-A España-Francia-Andorra (POCTEFA 2021-2027). Additional funding was provided by the Instituto de Salud Carlos III (ISCIII), grant number AC21_2/00024, as part of a grant from the European Joint Program for Neurodegenerative Research (JPND) JPND-2021-650-130. Additionally, CIC bioGUNE currently holds a Severo Ochoa Excellence accreditation, CEX2021-001136-S, also funded by MCIN/AEI /10.13039/501100011033. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
No full textUnderstanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted comprehensive genome-wide association studies (GWAS) followed by a cross-breed meta-analysis for 232 complex traits and a within-breed meta-analysis for 12 traits, using 28.3 million imputed sequence variants in 70 328 animals across 14 pig breeds. We identified 6878 quantitative trait loci (QTL) for 139 complex traits. Leveraging the Pig Genotype-Tissue Expression resource, we systematically investigated the biological context and regulatory mechanisms behind these trait-QTLs, ultimately prioritizing 14 829 variant-gene-tissue-trait regulatory circuits. For instance, rs344053754 regulates UGT2B31 expression in the liver and intestines, potentially by modulating enhancer activity, ultimately influencing litter weight at weaning in pigs. Furthermore, we observed conservation of certain genetic and regulatory mechanisms underlying complex traits between humans and pigs. Overall, our cross-breed meta-GWAS in pigs provides invaluable resources and novel insights into the genetic regulatory and evolutionary mechanisms of complex traits in mammals.This work was supported by the National Key R&D Program of China (2022YFF1000900 to Zhe Zhang), the National Natural Science Foundation of China (32022078 to Zhe Zhang), the China Agriculture Research System (CARS-35 to Zhe Zhang, J.L., Y.C., X. Liu., S.M. and X.D.), the Local Innovative and Research Teams Project of Guangdong Province (2019BT02N630 to Zhe Zhang), the Agriculture and Food Research Initiative Competitive grants (2022-67015-36215 to L.F.) from the USDA National Institute of Food and Agriculture, the USDA NIFA AFRI grant (2019-67015-29321 and 2021-67015-33409 to G.E.L.), ‘Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection’ of the USDA Agricultural Research Service (ARS) (appropriated project 8042-31000-112-00-D to G.E.L.), the SCINet project of the USDA ARS project (0500-00093-001-00-D), the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) (in part by AFRI grant numbers 2020-67015-31398 and 2021-67015-33409 to L.M.), the Australian Research Council's Discovery Projects (DP200100499 to R.X.), the grant from the Danish Research Council for Independent Research (DFF 1335-00127 to M.F. and P.K.M.), PID2020-112677RB-C21 awarded by MCIN/AEI/https://doi.org/10.13039/501100011033 (to M.B.) and the European Union's Horizon 2020 research and innovation program (the GENE-SWitCH project under grant agreement no. 817998 to D.C.P.). Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer. All the funders had no role in study design, data collection, analysis, decision to publish or preparation of the manuscript.info:eu-repo/semantics/publishedVersio
“Real Meat, Real Care” – 71st International Congress of Meat Science and Technology (ICoMST), August 2025, Girona, Catalonia, Spain
Get PDFThe International Congress of Meat Science and Technology (ICoMST) is the leading international congress in the field of Meat Science and Technology, held annually. In 2025, the 71st Edition of the Congress was held in Girona, Spain (Fig. 1), from 3rd to 8th of August, bringing together around 500 participants from over 40 countries. The congress offers a broad perspective, encompassing topics that span the entire meat production chain, from farm to fork. The topics were organized into eight main categories, allowing for a comprehensive exploration of the sector's most relevant scientific, technological, and societal issues: Traditional meat products and innovative trends, sustainability in meat production (including packaging), animal welfare and meat quality, carcass quality and innovation in abattoirs, emerging technologies in meat processing, muscle biology and biochemistry (including omics), safety and quality, society and consumers and, nutrition and health.info:eu-repo/semantics/publishedVersio
Evaluación de nuevas variedades de trigo blando de primavera
Get PDFEn este artículo se presentan los resultados de los ensayos de nuevas variedades de trigo blando de primavera realizados en el marco de la red Genvce (Grupo para la Evaluación de Nuevas Variedades de Cultivos Extensivos en España), durante las campañas 2022/23 y 2023/24.info:eu-repo/semantics/publishedVersio
Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology
Get PDFAlthough variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.EG’s contributions were supported by an Australian Government Research Training Program Scholarship, AIMOS top-up scholarship (2022) and Melbourne Centre of Data Science Doctoral Academy Fellowship (2021). FF’s contributions were supported by ARC Future Fellowship FT150100297.info:eu-repo/semantics/publishedVersio
Avançament de resultats de les varietats de blat de moro de cicle llarg per a gra
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Effect of in vitro gastrointestinal digestion on the antioxidant properties of fruit and vegetable powdered smoothies reinforced with WPC80
Get PDFThe development of novel powdered smoothies obtained by spray-drying (SD) technology can contribute to revaluing fruits and vegetables from seasonal surplus. The aim of this study was to evaluate the effect of in vitro gastrointestinal digestion (GID) on the retention, activity and bioaccessibility of key antioxidants of two smoothies elaborated with fruits (apple, orange and banana) or vegetables (pumpkin, apple and carrot), fortified with whey protein concentrate 80 g/100g (WPC80) and spray-dried. α-Tocopherol, ascorbic acid, polyphenol and flavonoid contents, and antioxidant capacity were determined in the smoothies reconstituted with water or semi-skimmed milk. Bioaccessibility and remaining antioxidant capacity after digestion was calculated. This study demonstrated contained smoothies were rich in sugar, protein and fibre. These smoothie powders retained most antioxidant properties intact. The reconstitution of smoothies with semi-skimmed milk means higher flavonoids and vitamin E content. In vitro GID showed a positive effect on the antioxidant properties of these smoothies by improving the bioaccessibility of TPC and favouring the scavenging ABTS radical, although the content of flavonoids and tocopherol was decreased. These results confirmed that powdered smoothies show high nutritional values and considerable antioxidant activity as a health-enhancing fortified food. Digestive simulations provide information on the potential bioaccessibility of antioxidants.This work was supported by the Ministerio de Ciencia, Innovación y Universidades and FEDER, Spain under the Project PID 2021-125533OR-C42.info:eu-repo/semantics/publishedVersio
Microbiological hazards associated with the use of water in the post-harvest handling and processing operations of fresh and frozen fruits, vegetables and herbs (ffFVH). Part 3 (Fresh-whole FVH process water management plan)
Get PDFWater used in post-harvest handling and processing operations is an important risk factor for microbiological cross-contamination of fruits, vegetables and herbs (FVH). Industrial data indicated that the fresh-whole FVH sector is characterised by very variable operational cycle duration (between 8 and 900 h), large product volumes (e.g. more than 6000 tonnes) and process water at 2.8–25.0°C. Intervention strategies were based on water disinfection treatments, mostly using chlorine-based disinfectants. Water replenishment was not observed within studied industries. The industrial data, which included 29 scenarios were used to develop a guidance for a water management plan (WMP) for the fresh-whole FVH sector. A WMP aims to maintain the fit-for-purpose microbiological quality of the process water and consists of (a) identification of microbial hazards and hazardous events linked to process water; (b) establishment of the relationship between microbiological and physico-chemical parameters; (c) description of preventive measures; (d) description of intervention measures, including their validation, operational monitoring and verification; and (e) record keeping and trend analysis. A predictive model was used to simulate water management outcomes, highlighting the need for water disinfection treatments to maintain the microbiological quality of the process water and the added value of water replenishment. Relying solely on water replenishment (at realistic feasible rates) does not avoid microbial accumulation in the water. Operational monitoring of the physico-chemical parameters ensures that the disinfection systems are operating effectively. Verification includes microbiological analysis of the process water linked to the operational monitoring outcomes of physico-chemical parameters. Food business operators (FBOps) should set up and validate a tailored WMP to identify physico-chemical parameters, as well as microbial indicators and their threshold levels, as performance standards for maintaining the fit-for-purpose microbiological quality of the process water during post-harvest handling and processing operations.info:eu-repo/semantics/publishedVersio
Targeting eEF1A reprograms translation and uncovers broad-spectrum antivirals against cap or m6A protein synthesis routes
Get PDFPlitidepsin is an antitumoral compound safe for treating COVID-19 that targets the translation elongation factor eEF1A. Here we detect that plitidepsin decreases de novo cap-dependent translation of SARS-CoV-2 and non-viral RNAs but affects less than 13% of the host proteome, thus preserving cellular viability. In response to plitidepsin, cells upregulate EIF2AK3 and proteins that reduce translation, but also proteins that support proteostasis via ribosome synthesis and cap-independent translation by eIF4G2 and IGF2BP2. While plitidepsin inhibits cap- or internal ribosome entry sites (IRES)-mediated translation, its impact on N6-methyladenosine (m6A) translation is limited. In agreement, plitidepsin blocks members of Coronaviridae, Flaviviridae, Pneumoviridae and Herpesviridae families. Yet, it fails to inhibit retroviruses that exploit m6A synthesis routes and are blocked by drugs targeting IGF2BP2 m6A reader. By deciphering the molecular fingerprint of cells treated with therapies targeting translation we identify a rational approach to select broad-spectrum antivirals with potential to counteract future pandemic viruses.N.I-U. is supported by the Spanish Ministry of Science and Innovation (grants PID2020-117145RB-I00, PID2023-147498OB-I00 and 10.13039/501100011033, Spain), EU HORIZON-HLTH-2021CORONA-01 (grant 101046118, European Union) and by institutional funding of PharmaMar, Grifols, HIPRA, and Amassence. E.M-M. is supported by the Spanish Ministry of Science and Innovation (grant PRE2021-099271). E.F-T is supported by JDC2023-050389-I funded by MCIU/AEI/10.13039/501100011033 and FSE+. E.G-V. is a research fellow from PERIS (SLT017/20/000090). E.B. and R.B. are research fellows from ISCIII-FIS (CPII19/00012; CP19/00011). K.K. is supported by funding from the Spanish Ministry of Research and Innovation (RYC2021-033035-I/AEI/10.13039/501100011033). G.C. is supported with funding from PLEC2022-009171/AEI/10.13039/501100011033. IrsiCaixa is supported by 2021 SGR 0045. The proteomic analyses were conducted at the IJC Proteomics Unit, which is affiliated with the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Spanish Platform of Molecular and Bioinformatics Resources (ProteoRed), Instituto de Salud Carlos III (PT17/0019), and CERCA GINYNS. This unit serves as a gateway to scientific and technical infrastructures. We acknowledge J. Díaz from the CMCiB for his constant help at the BSL3 facility. We thank the contribution of E. Martró and V. Saludes from the Microbiology department of HUGTIP for their constant help to identify and sequence SARS-CoV-2 variants. The authors also acknowledge the crowdfunding initiative #Yomecorono (https://www.yomecorono.com) and Foundation Dormeur for financial support for the acquisition of the QuantStudio-5 real-time PCR system and an Eclipse Ts2RFL inverted research microscope.info:eu-repo/semantics/publishedVersio
Climate change mitigation through irrigation strategies during rice growing season is off-set in fallow season
Get PDFNon-continuous flooding irrigation practices, such as alternate wetting and drying (AWD) and mid-season drainage (MSD), have been implemented in rice agroecosystems to reduce water use and mitigate climate change. Draining fields reduces methane (CH4) emissions, as soil aeration decreases the abundance and activity of soil methanogens. Mitigation effects during the growing season have been widely studied. However, there is a knowledge gap regarding potential effects these growing season practices might have on subsequent fallow season emissions. This is relevant when assessing overall annual CH4 emissions, particularly in systems in which fallow seasons account for a significant part of these. A field experiment was implemented in the Ebro Delta region (Catalonia, Spain) with the objective of identifying potential effects of growing season AWD and MSD on CH4 emitted during the following flooded fallow season, in comparison to continuously flooded fields. Both emissions and the structure of soil microbial communities were analyzed for rice field plots under the assessed irrigation strategies during the growing season and later for a continuously flooded mesocosm across the fallow season. Both practices achieved an average 86% decrease in CH4 fluxes when compared to continuous flooding during the growing season. AWD resulted in the highest fallow season emissions, leading to increases in overall annual cumulative CH4 emissions (+8%), global warming potential (+30%) and yield-scaled global warming potential (+70%) compared to continuous flooding. Growing season AWD decreased the relative abundance of both methanogens and methanotrophs in the fallow season. Reduced methanotroph communities might lead to lower CH4 consumption, resulting in higher fallow season emissions and offsetting the mitigation effect achieved during the growing season. Under the studied conditions, MSD represented a more effective mitigation strategy. These results highlight the importance of considering both rice growing and fallow season when assessing climate change mitigation strategies.This study was funded by the Spanish Ministry of Economy, Trade and Enterprise (MINECO) through the Grant PID2020-118650RR-C31 (funded by MCIN/ AEI/ 10.13039/ 501100011033). The Government of Catalonia funded the predoctoral fellwoship of S.E.-P. through the projects AgriCarboniCat and AgriRegenCat. N.P.-M. is supported by a Spanish ‘Ramón
Cajal’ fellowship (RYC-2021-033599-I). We thank Joan Noguerol for all his support in gas chromotagraphy analysis and Prof. Bruce A. Linquist for his reviews and constructive feedback. We also thank Andrea Bertomeu, Vicent Cebolla, Joan Didac Bertomeu, Raul Llevat, Guillem Rovira and Juan Blas Fernández-Araujo for all their field support. The support of the CERCA Programme, Generalitat de Catalunya, is also acknowledged.info:eu-repo/semantics/publishedVersio