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Towards safer fruit and vegetable products: Global meta-regression modelling of vegetative pathogen inactivation by non-thermal high-pressure processing
Get PDFThis study aimed to collect and meta-analyse data on inactivation of Escherichia coli, Salmonella and Listeria in
fruits and vegetables processed by high pressure (HPP) under non-thermal conditions (<45 ◦C). An extensive
literature search yielded 55 selected articles, 1633 Log reduction values were extracted and 97 DP (time for 1-log
reduction) were estimated. Time for 5-Log reduction (5DP) was also calculated, considering pressure come-up
inactivation, shoulder and biphasic behaviour. Pressure and product pH category explained 91–93 % data
variability, both being significant fixed effects factors along with microorganism. Random effects (study and
strain nested within microorganism) did not improve model fit. A global regression Bigelow-type model for
LogDP and Log5DP resulted in a LogDPref and Log5DPref parameter for each pH category and a common zP for all
microorganisms. The model’s predictive performance was assessed with 1126 independent Log reduction data.
Fail-dangerous predictions occurred in only 20 % of cases for E. coli, 6 % for Salmonella and 10 % for L. monocytogenes,
thus confirming the model as a conservative tool for risk assessment, benchmarking and setting HPP
parameters to meet a given performance criterion. At 600 MPa, up to 19 min are required to achieve 5-Log
reduction of vegetative pathogens in low-acid products, while 3 min and 1.5 min are sufficient for acid and
high-acid matrixes, respectively. A user-friendly decision support system prototype integrating the validated
model will assist stakeholders in setting and validating HPP conditions that comply with regulatory requirements
and ensure food safety in the production of fruit and vegetable-based foods.This work was supported by the SAFFI project (Safe Food for Infants in the EU and China), which has received funding from the European Union's Horizon 2020 research and innovation programme (GA 861917), SEQUSAL (2021 SGR 00468) and the CERCA Programme from Generalitat de Catalunya. Berta Torrents-Masoliver is recipient of a IRTA Sponsored Fellowship 2022.info:eu-repo/semantics/publishedVersio
Complementary strengths of water footprint and life cycle assessments in analyzing global freshwater appropriation and its local impacts – Recommendations from an Interdisciplinary discussion series
Get PDFConsidering globally increasing water challenges, the analysis of water use along supply chains is of great relevance and can be tackled by mainly two methodological approaches: Water Footprint Assessment (WFA) and Life Cycle Assessment (LCA). While sharing the same goal of promoting sustainable water use, both methods developed in different contexts and scientific communities. This has led to heated debates on methodological presuppositions that at times has become unconstructive. To build mutual understanding and enable a fruitful cooperation, researchers from both communities have exchanged over the course of two years. This paper summarizes the outcomes of this discussion series by providing i) a description of the development of both approaches and their ways of assessing freshwater consumption and pollution, ii) an application in a case study, and iii) an analysis of strengths and weaknesses in relation to questions decision-makers may have. Our analysis revealed that WFA’s strength lies in its ability to measure freshwater appropriation, water-use efficiency, water scarcity and total pollution levels. This makes WFA particularly useful for crop selection as well as agricultural and river basin water management. With its focus on assessing impacts, LCA is strong in quantifying potential consequences of water use for humans and ecosystems. This makes it particularly useful for assessing complex supply chains and for analysing water-related impacts in combination with other environmental aspects. Rather than being in competition with each other, we emphasize the individual and complementary strengths of both approaches and their joint efforts in addressing the world’s pressing water challenges.The authors thank Dr Lauren Seaby Anderson from the Potsdam Institute for Climate Research for providing data on evaporation from potential natural vegetation used for the case study in this paper. The authors from IRTA appreciate the financial support of the CERCA program (Generalitat de Catalunya), and the financial support of AGAUR (Generalitat de Catalunya) to the Consolidated Research Group “Sustainability in Biosystems” (no. ref. 2021 SGR 01568). Montserrat Nuñez thanks the Ramon y Cajal grant (RYC 2020) funded by the Spanish Ministry of Science and Innovation and the European Social Fund, “ESF Investing in your future”. Fatemeh Karandish would like to thank the financial support from European Union (ERC Starting Grant, GROW-101041110.info:eu-repo/semantics/publishedVersio
Quantitative characterization of high-pressure inactivation of E. coli and Salmonella in fruit purees enhanced by acid exposure and delayed sampling
Get PDFThis study aimed to quantitatively characterize the inactivation kinetics of Escherichia coli (CECT5947 & CTC1029) and Salmonella (GN001 & CIP106188) during high-pressure processing (HPP, from 300 to 600 MPa) in apple (pH 3.6) and banana (pH 4.2) purees. The impact of a 24 h-acid exposure before HPP and delayed sampling after HPP were addressed, as relevant scenarios for the food industry. Primary and secondary kinetic parameters were estimated by two- and one-step model fitting. HPP efficacy was both strain- and product-dependent, with greater inactivation in apple puree due to its higher acidity compared with banana puree. After 2 min at 400 MPa, E. coli CECT5947 was reduced 3.21 Log (apple) and 0.55 Log (banana), while CTC1029 strain showed reductions of 5.91 Log (apple) and 0.65 Log (banana). Salmonella CIP106188 was reduced by 4.2 Log (apple) and 1.5 Log (banana), while GN001 strain decreased 3.1 Log (apple) and 0.3 Log (banana). Our findings indicate that the inactivation during pressure come-up time should be considered when modelling the HPP bacterial inactivation. According to the model, pressure showed a quadratic effect on the inactivation during come-up time. Remarkably, acid exposure and a delayed sampling after HPP significantly enhanced the inactivation of both microorganisms. This study highlights the need of product-specific predictive models for setting tailored HPP conditions suitable to meet the 5 Log reduction performance criterion. The results emphasize that for validation and verification purposes, sampling for microbiological analysis can be performed 24 h after HPP to avoid underestimation of HPP efficacy in acid food matrixes.This work was supported by the SAFFI project (Safe Food for Infants in the EU and China), which has received funding from the European Union's Horizon 2020 Research and Innovation Programme (GA 861917), SEQUSAL (2021 SGR 00468) and the CERCA Programme from Generalitat de Catalunya. Berta Torrents-Masoliver is recipient of a IRTA Sponsored Fellowship 2022.info:eu-repo/semantics/publishedVersio
Morpho-physiological digestive features of genetically closely related sympatric lacustrine whitefish forms with different feeding habits
Get PDFThe effect of different feeding habits on gut morphology and digestive function has been intensively studied during the last decades but sympatric closely related fishes are relatively rare objects of such studies. In the present study, we have identified both morphological and physiological changes in the digestive system of a sympatric pair of whitefish represented by “normal” Coregonus lavaretus pidschian (benthivorous) and “dwarf” C. l. pravdinellus (planktivorous) forms. There were statistically significant differences in terms of histometric variables between segments of the stomach (height of lining epithelium, fold thickness and height values, and number of folds) and intestine (enterocyte height and fold height) within each form as well as between forms for the same segment of the digestive tract like in the stomach (height of lining epithelium and fold thickness) and intestine (enterocyte height, fold height and fold thickness). Both forms had a similar number (8–9 bands) and molecular weight of isoforms/isoenzymes of alkaline proteases inhibited by PMSF (serine proteases) based on zymogram analyses. The maximum level of activity of alkaline proteases, alkaline phosphatase, and aminopeptidase N were registered in the pyloric caeca for both forms. In contrast to these enzymes, the activity of α-amylase as well as of non-specific lipases and esterases in the pyloric caeca was similar or even lower if compared to other intestinal segments. In conclusion, both sympatric forms of whitefish showed some similarities in several of studied biochemical and histological parameters of their digestive tracts, regardless of their different feeding habits, which might be related to their genetical background.The acquisition of field samples, and the biochemical and histomorphological analyses conducted in this study were supported by the Russian Science Foundation (grant number 23–74-10101). The meta-analysis of the results was supported by the Russian international scientific collaboration program Mega-grant (No. 075–15-2022–1134).info:eu-repo/semantics/acceptedVersio
Deep Sequencing Reveals Dual Evolution of SARS-CoV-2: Insights Into Defective Genomes From Wuhan-Hu-1 Variants to Omicron Subvariants
Get PDFSARS‐CoV‐2 has evolved from early variants dominating the first (B.1.5, B.1.1) and second (B.1.177) pandemic waves, which
exhibited a higher frequency of minority mutants with deletions leading to Defective Viral Genomes (DVGs) in the spike region
near the S1/S2 cleavage site than the Alpha, Beta, and Delta variants. The emergence of Omicron has significantly altered the
dominant variant profile, with Omicron subvariants now representing 100% of circulating viruses. To monitor the evolution and
adaptation of Omicron in the human population, a deep‐sequencing study was performed in RNA samples of BA.1, BA.1.1,
BA.2, BA.5, BQ.1.1, XBB.1.5 and BA.2.86 Omicron subvariants. The findings reveal two occurrences of similar evolutionary
patterns within SARS‐CoV‐2 characterized by a shift from a significant to a very low production of DVGs. This event suggests
that DVGs might play a role in the virus's spread and adaptation for persistence in infected humans.This study was supported by Spanish Ministry of Education, Centro para el Desarrollo Tecnológico Industrial (CDTI), Fondo de Investigación Sanitaria, Spanish Ministry of Economy and Competitiveness, Fundació Institut de Recerca Hospital Universitari Vall d'Hebron, 'la Caixa' Foundation, Consorcio Centro de Investigación Biomédica en Red (CIBER), and Early Response and Rapid Action Zoonotic Emergencies Program (ERRAZE).info:eu-repo/semantics/publishedVersio
Interactive effects of high n-3 PUFA intake and cyclic heat stress under two dietary antioxidant levels in broiler chickens
Get PDFThe study examined the combined effects of a diet high in n-3 PUFAs and
cyclic heat stress (HS) considering two levels of dietary antioxidants. A total of
192 one-day-old male Ross 308 broilers were divided into eight groups in a 2
× 2 × 2 factorial design: thermoneutral (TN) or heat-stressed (34°C ± 1°C for
7 h/day from day 22) × fed a diet low in antioxidants (NRC group) or high in
antioxidants (HAOX group; supplemented with a mixture of 200 IU/kg vitamin E,
250 mg/kg vitamin C and 0.15 mg/kg selenium) and supplemented or not with
5% linseed oil, forming the NRC N-3 and HAOX N-3 groups. High intake of n-
3 PUFAs increased plasma F2-isoprostane and malondialdehyde (MDA) levels
and superoxide dismutase (SOD) activity. Cyclic HS decreased final body weight
(BW) and average daily feed intake (ADFI) and increased DNA damage and serum
corticosterone (CORT) levels. In addition, the changes in blood biochemistry
indicated that the broilers were undergoing respiratory alkalosis. Interactions
between n-3 PUFAs and HS were observed in liver MDA levels, plasma γ-
tocopherol levels and serum alkaline phosphatase (AP) activity. Antioxidants
increased blood levels of α-tocopherol, vitamin C, lipid- and water-soluble
antioxidants and glutathione peroxidase (GPx) activity, while decreasing MDA,
F2-isoprostane, CORT and AP levels. High intake of n-3 PUFA in combination
with cyclic HS had negative effects on the health status of the broilers, which
were alleviated by additional antioxidant supplementationThe author(s) declare that financial support was received for the research and/or publication of this article. This research was funded by The Slovenian Research and Innovation Agency, grant numbers: P4-0097 and P4-0053info:eu-repo/semantics/publishedVersio
Comprehensive MSI-based protocols for the spatial lipidomics characterization of microscale organisms
Get PDFSpatial omics technologies are essential for characterizing molecular disruptions induced by pathological conditions or environmental stressors while preserving the native spatial context of biomolecules. Among these, mass spectrometry imaging (MSI) has become a central platform for spatial lipidomics. However, applying MSI to small and fragile organisms, such as zebrafish embryos (ZFEs), presents significant challenges. In this study, we introduce an integrative MSI-based workflow for spatial lipidomics, optimized for ZFEs but broadly adaptable to other delicate biological microsystems. The workflow integrates a refined sample preparation protocol that enabled high-quality consecutive tissue sections with a systematic comparison of ionization strategies, including matrix-assisted laser desorption/ionization (MALDI), surface-assisted laser desorption/ionization (SALDI), and advanced laser post-ionization (MALDI-2), achieving reproducible multimodal MSI analysis. Beyond comparative assessment, our results provide new insights into the ionization yields for each MSI platform. MALDI-2 stands out as a technique for spatial lipidomics, demonstrating superior ionization efficiency and enabling high-resolution imaging down to a pixel size of 5 μm. This pixel size enhancement improves visualization of anatomical structures and detailed lipid mapping, which are critical for understanding lipid biology in these small models. While MALDI proved highly effective for glycerophospholipids and sphingolipids, SALDI showed better performance for low-molecular-weight and neutral lipids. These results establish a conceptual model linking experimental conditions and analyte properties to optimize ionization across lipid classes, providing a robust framework for MSI-based spatial lipidomics in ZFEs. Therefore, this advancement contributes to the broader application of spatial omics using novel biological systems on biomedical, pharmacological and toxicological research.The research leading to these results has received funding from the Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033, PID2021-122929OB-C33 and CEX2018-000794-S. C·B has been supported by the European Union (MASS2 101067953 - HORIZON-MSCA-2021-PF-01). AMP also acknowledges a grant PRE2020-094656 funded by MCIN/AEI/10.13039/501100011033 by ESF Investing in your future. M.G.A acknowledges the grant RYC2022-036211-I funded by MICIU/AEI/10.13039/501100011033. The authors also acknowledge BioRender for providing the tools to create some of the illustrations included in this work.info:eu-repo/semantics/publishedVersio
Mushroom stem-based diets elicit region-specific shifts in rainbow trout gut microbiota
Get PDFThe intestinal microbiota of fish plays a crucial role in host condition and health, exhibiting region-specific functions influenced by dietary components. This study evaluated the effects of mushroom stem meals from Agaricus bisporus (AB), Lentinula edodes (LE), and Pleurotus ostreatus (PO), used as sustainable ingredients on the intestinal microbiota and histomorphology of rainbow trout (Oncorhynchus mykiss). Experimental diets containing 30% mushroom stem meals were tested for 42 days under standard conditions in juvenile rainbow trout (120.1 ± 0.4 g). Mushroom stem meals did not affect the integrity of the intestinal mucosa while inducing a subtle region-specific shift in the intestinal microbial communities. These changes were reflected in intra-individual and inter-individual diversity differences among diets. Specifically, Shannon index decreased in the pyloric caeca (PC), anterior (AI) and posterior intestine (PI) of fish fed the AB diet, while the observed richness and Faith’s phylogenetic diversity showed a reduction in the AI and PI regions of fish fed the LE diet. Regarding composition, a consistent pattern found across the three intestinal regions was the high abundance of Desulfobacterota in fish fed the control diet (0% mushroom stem meals). Regarding the mushroom stem-based diets, the AB diet promoted an increase in the abundance of potentially beneficial bacteria, such as Mycoplasma in the PC and AI, Legionella exclusively in the AI, and Weissella in the PI. In contrast, the PO diet increased the abundance of Paenibacillus in the PC, while the LE diet did not markedly alter genus-level abundances. Region-specific patterns suggested microbial shifts in the PC were related to digestion and nutrient metabolism, while changes in the AI may reflect transient colonization by diet-derived bacteria linked to niche specialization. The PI microbiota was comparatively conserved and associated with carbohydrate fermentation. These findings provide insights into the region-specific effects of circular dietary ingredients and highlight the potential use of mushroom stem meals as functional ingredients due to prebiotic effect as they beneficially modulate the intestinal microbiota and support gut health in rainbow trout.The author(s) declare that financial support was received for the research and/or publication of this article. This work was conducted within the GreenBlueCircle project (TED2021-132054B-C21/C22) funded by the Ministerio de Ciencia e Innovación (Spain). Carl John Saromines was supported by a predoctoral grant from IRTA. Silvia Torrecillas is financed by a Ramón y Cajal fellowship (RYC2021-031414-I) funded by MICIU/AEI/https://doi.org/10.13039/501100011033 and, as appropriate, by “ESF Investing in your future”, by “ESF+” or by “European Union NextGenerationEU/PRTR”.info:eu-repo/semantics/publishedVersio
Analysis of Ciguatoxins in Fish with a Single-Step Sandwich Immunoassay
Get PDFCiguatoxins (CTXs) are the primary cause of ciguatera poisoning (CP), one of the most prevalent non-bacterial seafood-borne illnesses worldwide. With no cure available beyond palliative treatments to alleviate symptoms, effective CP management relies on prevention. However, the detection of CTXs in seafood poses significant analytical challenges due to their typically low concentrations in specimens and the high variability among CTX congeners, many of which remain poorly characterized. These challenges have led to a growing demand for the development of rapid, sensitive, and user-friendly bioanalytical tools for CP surveillance. In this study, several simplified sandwich immunoassay strategies were evaluated for the detection of Pacific CTXs in fish. Among them, the single-step strategy was identified as the most promising, as it enables the detection of Pacific CTXs in complex fish matrixes within only 40 minutes at levels as low as 0.01 µg CTX1B equivalents/kg of fish, aligned with the safety guidance level proposed by the United States Food and Drug Administration (FDA). Unlike traditional sandwich immunoassays, which require several sequential incubation steps, the single-step strategy involves a simultaneous incubation of all components with the sample, uniquely followed by a washing and substrate incubation step prior to signal measurement. This approach significantly reduces both the complexity and time required for analysis, positioning this immunoassay as a highly promising tool for CP risk assessment and management.info:eu-repo/semantics/publishedVersio
The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project
Get PDFGenetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.L. Fang is supported by Agriculture and Food Research Initiative Competitive grant 2022-67015-36215 from the USDA National Institute of Food and Agriculture, and seed funding from CellFood Hub (Aarhus University Foundation). Y. Luo is supported by the Innovative Health Initiative Joint Undertaking under grant agreement 101165643. Z. Zhang is supported by funding from the China Agriculture Research System (CARS-35). We thank all the researchers who have contributed to the generation and analyses of both publicly available and newly generated data used in the pilot phase of FarmGTEx. We thank I. Kaplow at the Department of Biological Sciences and the Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University for valuable comments on the manuscript.info:eu-repo/semantics/acceptedVersio