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Spatial distribution of pollutants along the Galician coast: Insights from starfish bioindicators
Full text linkIdentifying suitable aquatic organisms for biomonitoring of marine waters is crucial for effective environmental management. In this study, for the first time in the region, starfish were used as bioindicator of water quality to evaluate the Galician coast, with rich biodiversity and one of the largest maritime import hubs in Europe. For this purpose, this study focused on two common starfish species in the area: Marthasterias glacialis and Asterias rubens. Samples were collected between January and February 2021 from eight specific locations along the Galician coast, each characterized by unique features and varying levels of anthropogenic pressure. The analysis included 17 organochlorine pesticides (OCPs), as well as 17 trace elements. Notably, and for the first time in this context, saponins and marine toxins (including amnesic, lipophilic and paralytic toxins) were also analyzed in all collected samples. The results revealed that concentrations of inorganic and organic compounds in starfish were comparable to those found in other organisms traditionally used as bioindicators in the same region, such as mussels and oysters. Moreover, the obtention of saponin content at different sampling sites allows for comparisons among areas, making it possible to assess whether significant differences exist. Based on the levels of anthropogenic pressures, interspecies variations and the sensitivity of these organisms to these pollutants, this study concludes that starfish have strong potential as bioindicators for monitoring water quality along the Galician coast. They could be integrated into existing coastal monitoring programs, such as those under the Marine Strategy Framework Directive, providing complementary information alongside traditional bioindicators.This work was funded by the project “Strategies for the Valorization of the Starfish” (ACUISTAR), with the support of Fundación Biodiversidad, Ministerio para la Transición Ecológica y el Reto Demográfico, through Programa Pleamar co-financed by Fondo Europeo Marítimo y de Pesca (FEMP). The authors acknowledge support from the CERCA Programme/Generalitat de Catalunya, and thank Laura Ferreres and Anna Safont for their technical support. We also gratefully acknowledge the technical assistance of Alicia López and Belén Fandiño, and the collaboration of the Fishermen's Guilds (Cofradías de Pescadores) of Galicia.info:eu-repo/semantics/publishedVersio
Co-occurring microbial guilds in pig fecal microbiota: key drivers and effects on host performance
Full text linkBackground The pig gut microbiota is a complex ecosystem composed of microbial guilds that remain largely unexplored.
Here we decomposed the pig fecal microbiota of two cohorts of 648 healthy Duroc pigs during the transition
(n = 400) and growing finish (n = 248) periods in co-occurring bacterial guilds defined as pig enterosignatures (ES).
Results Our results indicate that fecal microbial ecosystems can accurately be described by combinations
of at least six ES, driven by the Prevotella (ES-Prev), Treponema (ES-Trep), Lactobacillus (ES-Lact), Clostridium (ES-Clost),
Streptococcus (ES-Strep), and UBA2810 (ES-UBA2) genera. We observed a dynamic shift with age in the composition
of ES, where ES-Prev, ES-Strep, and ES-Lact seem to be core components. Our results suggest partial genetic
control by the host, with heritabilities of ES composition ranging from 0.24 to 0.36. Furthermore, our findings indicate
that stress on the host is associated with assembly of the ES, decreasing ES-Lact abundance, and increasing
prevalence of ES-Strep. We noted a positive association of ES-Prev with growth rate at 60-days, which later evolved
to become negative, impacting feed efficiency during the growing period. Remarkably, a negative association
of the abundance of ES-Lact with levels of hair cortisol was also found during this period.
Conclusions Our findings provide novel insights into the pig gut microbiota and reveal novels associations with relevant
porcine physiological and performance traits. Moreover, while the ES concept has proven valuable in dissecting
microbial communities into assemblies of underlying microbial guilds, our results emphasize the relevance of customizing
microbial interventions strategies based on the nutritional and health requirements at each stage of the porcine
production cycle.ITV was funded by the HoloRuminant (101000213) and GEroNIMO (101000236) H2020 projetcs. AC was funded with a PhD fellowship (PRE2022-101829) awarded by the Spanish Ministry of Education and Culture. YRC received the “Ramon y Cajal” grant (RYC2019-027244-I) funded by MCIN/AEI/https://doi.org/10.13039/501100011033 and by “ESF Investing in your future”. Part of the research presented in this publication was funded by Grants AGL2017-88849-R, PID2020-112677RB-C21and PID2021-126555OB-I00 awarded by the Spanish Ministry of Economy and Competitiveness.info:eu-repo/semantics/publishedVersio
Heat Stress and Betaine Affect Lipolysis in Pig Adipose Tissue Explants
Full text linkHeat stress (HS) is an environmental variable challenging pig production worldwide.
It may alter carcass composition by increasing fat deposition but the mechanisms are
poorly understood. Betaine is a metabolic modifier able to decrease carcass fat in pigs,
but the effects of betaine on lipolysis under high temperatures are not known. Our goal
was to determine a potential effect of betaine on lipolysis in the fat tissue of Iberian pigs
under thermoneutral (TN) or HS conditions. Eight pigs (89 kg BW) were used to obtain
explants from dorsal subcutaneous adipose tissue. Explants were cultivated under TN
(37 ◦C) or HS conditions (41.5 ◦C) for 1.5 h to study direct effects of HS on acute lipolysis.
Treatments included control and betaine addition (200 µM). Indirect effects of HS were
examined using the culture medium amended with 1 µM isoproterenol ±10 nM insulin
in the presence or absence of betaine and HS. Media glycerol was measured at the end
of the incubations as a proxy of lipolysis. HS decreased basal lipolysis (−47%; p < 0.001)
but increased isoproterenol-stimulated (a β-agonist) lipolysis (+31%; p < 0.01). Betaine
increased non-stimulated lipolysis both under TN and HS conditions (73%; p < 0.001). As
expected, isoproterenol augmented lipolysis both in TN (2714%; p < 0.001) and HS (3589%;
p < 0.001) conditions. The addition of insulin to lipolysis-stimulated explants analogously
diminished glycerol release in TN (−39%; p < 0.001) and HS (−50%; p < 0.001) conditions.
In conclusion, HS reduced non-stimulated lipolysis in Iberian pigs in line with increased
adipose tissue accretion, while betaine partly increased lipolysis, counteracting the effects
of HS. Betaine supplementation could be a strategy to counteract HS-induced fattening
in pigs.This research was funded by Ministerio de Economía y Competitividad, grant no. AGL 2016-80231. Z. Pardo received a scholarship FPI from Ministerio de Economía y Competitividad (reference BES-2017-081486) and was part of the PhD Thesis project within the Official Doctorate Program of Nutrition and Food Sciences (University of Granada, Spain).info:eu-repo/semantics/publishedVersio
Empowering bioinformatics communities with Nextflow and nf-core
Full text linkStandardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.The EuroFAANG genomics communities have received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement Numbers 817923 (AQUA-FAANG), 815668 (BovReg), 817998 (GENE-SWitCH), 101000226 (RUMIGEN), 101000236 (GEroNIMO), 101000213 (HoloRuminant), and the Horizon Europe programme under Grant Agreement Number 101094718 (EuroFAANG Research Infrastructure). Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.
Horizon 2020 research and innovation programme,European Union,815668 (BovReg),815668 (BovReg),817923 (AQUA-FAANG),815668 (BovReg),815668 (BovReg),815668 (BovReg),817998 (GENE-SWitCH),101000236 (GEroNIMO),815668 (BovReg),817998 (GENE-SWitCH),817923 (AQUA-FAANG),817923 (AQUA-FAANG),817998 (GENE-SWitCH),815668 (BovReg),817998 (GENE-SWitCH),815668 (BovReg),817998 (GENE-SWitCH),817923 (AQUA-FAANG),817923 (AQUA-FAANG),815668 (BovReg),101000236 (GEroNIMO),101000213 (HoloRuminant),815668 (BovReg),815668 (BovReg),815668 (BovReg),815668 (BovReg),815668 (BovReg),Spanish Ministry of Science and Innovation,Generalitat de Catalunya,Werner Siemens-Stiftung,Palaeobiotechnology,Horizon Europe programme,European Union,101094718 (EuroFAANG Research Infrastructure),101094718 (EuroFAANG Research Infrastructure),Carl-Zeiss-Stiftung,Certification and Foundations of Safe Machine Learning Systems in Healthcare,Deutsche Forschungsgemeinschaft,EXC 2180—390900677 (iFIT)
CN, BL and JEC have received funding from the Spanish Ministry of Science and Innovation. They acknowledge support from the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI/https://doi.org/10.13039/501100011033), and the Generalitat de Catalunya through the CERCA programme. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the grant agreement 815,668 (BovReg). They are grateful to the CRG Core Technologies Programme for their support and assistance in this work.
SN acknowledges support by the Carl Zeiss Foundation, project “Certification and Foundations of Safe Machine Learning Systems in Healthcare.” SN is “gefördert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Länder—EXC 2180—390,900,677 (iFIT).” SN is “gefördert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Länder—EXC 2124–390,838,134 (CMFI).” This study was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the project NFDI 1/1 “GHGA—German Human Genome-Phenome Archive” (#441,914,366 to SN).
J.A.F.Y. was supported by Max Planck Society and the Werner Siemens Foundation grant “Palaeobiotechnology” (awarded to Profs. Pierre Stallforth and Christina Warinner).info:eu-repo/semantics/publishedVersio
Compositional analysis of alternative protein blends using near and mid-infrared spectroscopy coupled with conventional and machine learning algorithms☆
Full text linkThe non-invasive real-time analysis of the composition of alternative, plant-based protein sources is important to control high moisture extrusion processes and ensure the quality and texture of the final extrudates used in the elaboration of meat analogues. This study aims to analyse the composition and presence of gluten in blended plant-based alternative protein sources from pulse, cereal and pseudocereal origin by means of near infrared spectroscopy (NIRS) and mid infrared spectroscopy (MIRS) using conventional and machine learning algorithms. Blends were prepared using five alternative protein sources (barley, wheat, fava bean, lupin, and buckwheat) and spectra were acquired using a low-cost and a benchtop near-infrared spectrometer, and a mid-infrared spectrometer. Using the acquired spectra, partial least square regression (PLSR), support vector machine discriminant analysis (SVM-DA), partial least square discriminant analysis (PLS-DA), and convolutional neural networks (CNN) were used to develop predictive models to determine the composition and to identify samples containing gluten. The protein, moisture, carbohydrates and fat content in blends of alternative protein sources was determined with a RMSEP of 1.59, 0.18, 1.41, and 0.19 %, respectively, when using the benchtop NIR spectrometer and PLSR. Gluten-free samples were identified with high sensitivity (0.85) and accuracy (0.93) using PLS-DA. The study demonstrated that infrared spectroscopy can be used to analyse the composition of blends of alternative protein sources including pulses, cereals, and pseudocereals, as well as to identify gluten-free samples.This research was supported by project Sensanalog [PID2021-122285OR-I00] funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU. The first author received the grant [PRE2022-103798] funded by MICIU/AEI/10.13039/501100011033 and ESF+. Acknowledgements are extended to the consolidated research group (2021 SGR 00461) and CERCA program from Generalitat de Catalunya. Elena Fulladosa was supported by a mobility grant within the Incentives for Research Program 2023 by the Institute of Agrifood Research and Technology (IRTA).info:eu-repo/semantics/publishedVersio
Differential LTR‑retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium)
Full text linkBackground
Transposable elements are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domestication, and crop improvement. Here, we implement genome and pangenome analyses to study in detail the dynamics of LTR-retrotransposons during the cotton evolution.
Results
We show that some LTR-retrotransposon lineages amplified in tetraploid cotton compared to their diploid progenitors, whereas others stayed stable or amplified but were removed through solo-LTR formation. Using species-level pangenomes we show that only a few lineages (CRM, Tekay, Ivana, and Tork) remained active after polyploidization and are still transposing. Tekay and CRM elements have re-shaped the centromeric and pericentromeric regions of tetraploid cottons in a subgenome specific manner, through new insertions but also selective eliminations through solo-LTR formation. On the other hand, Ivana and Tork have actively inserted within or close to genes affecting their expression. Finally, population-level analyses using the two pangenomes and data from 283 and 223 varieties of G. hirsutum and G. barbadense reveal changes in Transposon Insertion Polymorphism frequencies accompanying domestication and improvement of both species, suggesting the possibility of selection on linked regions.
Conclusions
Our findings reveal that LTR-retrotransposon lineages followed differential dynamics during cotton evolution, displaying differences among species and the two coresident genomes of allopolyploid cotton. A handful of the LTR-retrotransposon lineages that expanded after polyploidization helped shape the genomes of both G. hirsutum and G. barbadense, impacting their centromere and pericentromeric regions as well as protein-coding genes.This work was supported by PID2022-143167NB-I00 grant funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU to JC. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 945043 through the Postdoctoral Fellowship awarded to L.C.-D. by the AGenT H2020-MSCA-COFUND-2019 programme co-funded by the grant CEX2019-000902-S funded by MICIU/AEI/10.13039/501100011033. RC’s work was supported by his Ramón y Cajal fellowship (RYC2022-037459-I) funded by MICIU/AEI/10.13039/501100011033 and by ESF +. We acknowledge support on cotton research and polyploidy from the National Science Foundation, and we would also like to acknowledge Iowa State University Research IT for computational support.info:eu-repo/semantics/publishedVersio
Efficacy of a Novel PCV2d and Mycoplasma hyopneumoniae Combined Vaccine in Piglets with High and Low Levels of PCV2 Maternally Derived Antibodies at Vaccination
Full text linkBackground/Objectives: Maternally derived antibody (MDA) levels of porcine circovirus 2 (PCV2) may eventually interfere with humoral response and vaccination efficacy. This study aimed to evaluate the efficacy of a ready-to-use PCV2d and Mycoplasma hyopneumoniae combined vaccine in piglets with different PCV2 MDA levels at vaccination in an experimental inoculation with a heterologous viral genotype. Methods: Forty-eight piglets were allocated into vaccinated (V) and non-vaccinated (NV) groups with high (H) and low (L) PCV2 MDA subgroups (H-V, H-NV, L-V, L-NV). At 3 weeks of age, the piglets received either one dose of vaccine or placebo. Five weeks later, all animals were intranasally challenged with a PCV2b inoculum. Body weight was registered at different time points. Blood samples, peripheral blood mononuclear cells and tracheobronchial lymph nodes (TBLN) were collected and used to assess viraemia, viral load, humoral and cellular responses and histological lesions. Results: The V group showed higher PCV2 antibody levels from challenge onwards, along with a lower percentage of viraemic pigs and reduced viral load in serum at 2 and 3 weeks post-challenge (wpc) and in TBLN tissues compared to the NV group. The H-V group had the highest antibody levels post-challenge, showed no detectable viraemia and had a lower overall amount of virus in tissues. The NV group (especially H-NV) exhibited increased levels of IFN-γ, IFN-α and TNF-α post-challenge. Conclusions: The tested vaccine elicited humoral and cellular immune responses and reduced viral presence in serum and tissues, demonstrating efficacy in a PCV2 subclinical infection model despite high MDA levels at the time of vaccination. Understanding both humoral and cellular immune responses according to different MDA levels can help design more effective vaccination strategies against PCV2.
Keywords: porcine circovirus 2; maternally derived antibodies; vaccine; cytokines; quantitative PCR; in situ hybridisationinfo:eu-repo/semantics/publishedVersio
Animal welfare certification schemes in a knowledge society: A fair transition from inputs to outputs as a driver of animal empowerment
Full text linkAlthough concern for animal welfare may have been linked to humans since the domestication of livestock, the term itself first appeared in the United Kingdom in the 1960s. The emergence of the concept of animal welfare occurred in a society undergoing a clear transition from patriarchal to emancipatory values based on the concept of freedom. However, coinciding with the recognition of animals as sentient beings in the EU and the emergence of concepts such as a “Life Worth Living”, the Five Freedoms were complemented. In fact, the values of a knowledge society—through autonomy, justice, and equality—create the conditions for a society more connected to its emotions. This entire movement culminated in an updated and complementary definition called “the Five Domains,” in which the mental states of animals and their emotions are essential. However, in the meantime, the market is dominated by several animal welfare certification schemes that focus on inputs (what humans provide) rather than outcomes (animal-based indicators), reflecting an anthropocentric perspective that does not consider the actual experiences of animals from farm to farm. In a knowledge society, where emotions are so important, this approach will be considered unacceptable someday.info:eu-repo/semantics/publishedVersio
Enhancing soil organic carbon and structure in Mediterranean rice systems through cover cropping
Full text linkCover crops (CC) are recognized for their role in preventing and remediating soil degradation, yet their effects in Mediterranean rice (Oryza sativa L.) systems remain uncertain. This study evaluated the impact of ryegrass (Lolium multiflorum Lam.; RG) and hairy vetch (Vicia villosa Roth; HV) as winter CC on soil organic carbon (SOC) dynamics and physical properties of a Calcaric Fluvisol over three years. The effects were compared to a dry bare fallow (BF), with and without nitrogen (N) fertilizer application to rice. Cover cropping increased topsoil SOC levels (p = 0.015), with particulate organic matter as the primary driver (p = 0.039). Longer periods of cover cropping may be needed for a more prominent effect on mineral-associated organic matter dynamics and C sequestration. While both CC increased aggregation after incorporating rice residues by 17 % (p = 0.005), ryegrass demonstrated a more persistent improvement by also enhancing aggregation at CC termination (p = 0.013). However, hairy vetch may offer greater long-term benefits to soil quality potentially by supporting higher CC and rice residue inputs. Soil penetration data suggests constraints to CC root growth in conventional rice systems and highlights the need to integrate CC with other sustainable management practices to maximize their benefits. This study underscores how winter CC can enhance soil organic matter and restore soil quality of Mediterranean rice systems, despite the limiting conditions for growth.This work was funded by the Kellogg’s Origins Program, University of Lleida and Agrotecnio Research Center. This research work was also financially supported by the Ministry of Science, Innovation and Universities of Spain through the DISOSMED project [grant number AGL2017–84529-C3–3-R] and the SINTMED project [grant number PID2021–126343OB-C33]. G. Nascimento is a recipient of an UdL-IRTA PhD fellowship. The IRTA authors acknowledge the CERCA program (Generalitat de Catalunya) contribution.info:eu-repo/semantics/publishedVersio
Resultats de les noves varietats de blat tou de primavera
No full textS’ha observat un comportament diferent de les varietats en funció de la zona d’assaig. Al litoral de Girona han mostrat molt bon comportament productiu RGT MACARENO, RGT PISTOLO i LG ANCIA; amb tres anys de dades també LG BAROJA i ACUNA. Als regadius de Lleida les varietats més productives han estat CHAMBO i RGT TOCAYO i amb tres anys també LG REVENTON i ESPERADO, tot i que sense diferències significatives. Destaca la precocitat de LG ACORAZADO i LG TEMPERO, i l’alçada d’ALAMINOS. Els majors continguts en proteïna s’han observat amb ACA320, LG ACORAZADO i LG MASAYA, i són també les varietats que han mostrat una millor aptitud per a panificació.info:eu-repo/semantics/publishedVersio