355 research outputs found

    Application of metabolomic profiling and fingerprinting approaches to food fraud cases

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    [eng] Food fraud is an intentional and misleading act in food that generally does not comply with food law and is motivated by economic gain. It encompasses several fraudulent practices such as deception during manufacture, diversion into illicit supply chains, interventions with the food product, or misrepresentation. In this context, the coming to light of the horse meat scandal at the beginning of 2013 highlighted the shortcomings of the European system against food fraud, increasing concern and interest among European citizens and administrative bodies. Under these circumstances, in recent years, omics tools —comprising genomics, transcriptomics, proteomics, metabolomics, and elementomics/isotopollomics— have been applied to solve food fraud issues, along with biostatistics and chemometrics. In most cases, their application has relied on profiling (focusing on determining targeted secondary chemical markers) or fingerprinting approaches (based on the unspecific detection of instrumental responses without assuming any previous knowledge about the sample composition), overcoming the traditional targeted analysis. In particular, since a food product’s metabolome varies according to its biological nature and several external conditions (i.e., either from a natural or anthropogenic origin), metabolomics has shown excellent potential to assess several issues related to its authenticity and quality. Therefore, in this thesis, several metabolomic profiling and fingerprinting approaches were developed to address different food fraud cases. In this line, liquid chromatography coupled to low- or high-resolution mass spectrometry (LC–LRMS, LC–HRMS) was proposed for the targeted approaches. In contrast, non-targeted methods were based on liquid chromatography with ultraviolet detection (LC-UV) or fluorescence detection (LC-FLD), LC–HRMS, or direct mass spectrometry (MS)-based techniques. Furthermore, non-supervised and supervised chemometric techniques allowed sample assignation and classification. As a result, the proposed analytical methodologies were successfully applied to several food products —including paprika, nuts and seeds, hen eggs, vegetable oils, and red wine— guaranteeing their classification and authentication regarding the geographical origin, botanical origin, production system, or quality category.[cat] El frau alimentari és un acte intencionat i enganyós produït en els aliments que, generalment, no compleix amb la legislació alimentària i que està motivat per un benefici econòmic. La sortida a la llum de l’escàndol de la carn de cavall a principis del 2013 va posar de manifest les mancances del sistema europeu contra el frau alimentari, augmentant la preocupació i l’interès entre els ciutadans i els organismes administratius europeus. En aquestes circumstàncies, en els darrers anys, s’han aplicat eines òmiques —que inclouen la genòmica, la transcriptòmica, la proteòmica, la metabolòmica i l’elementòmica/isotopol·lòmica— per resoldre qüestions relacionades amb el frau alimentari, juntament amb bioestadística i quimiometria. En la majoria dels casos, la seva aplicació s’ha efectuat mitjançant estratègies basades en perfils (centrant-se en la determinació dirigida de marcadors químics secundaris) o empremtes dactilars (basades en la detecció inespecífica de respostes instrumental sense assumir cap coneixement previ sobre la composició de la mostra), superant l’anàlisi dirigida tradicional. En concret, com que el metaboloma d’un producte alimentari varia segons la seva naturalesa biològica i un seguit de condicions externes (siguin d’origen natural o antropogènic), la metabolòmica ha demostrat un excel·lent potencial per avaluar diverses qüestions relacionades amb la seva autenticitat i qualitat. En aquesta tesi, es van desenvolupar diverses estratègies de perfils i empremtes dactilars metabolòmiques per abordar alguns casos de frau alimentari. Així, es va proposar la cromatografia líquida acoblada a l’espectrometria de masses de baixa o alta resolució (LC–LRMS, LC–HRMS) per als enfocaments dirigits. En canvi, els mètodes no dirigits es van basar en la cromatografia líquida amb detecció ultraviolada (LC-UV) o fluorescent (LC-FLD), LC–HRMS o tècniques basades en l’espectrometria de masses (MS) directa. A més, tècniques quimiomètriques no supervisades i supervisades van permetre l’assignació i classificació de les mostres. Com a resultat, les metodologies analítiques proposades es van aplicar amb èxit a diferents productes alimentaris —incloent el pebre vermell, fruits secs i llavors, ous de gallina, olis vegetals i vi negre— garantint-ne la classificació i autenticació pel que fa a l’origen geogràfic, l’origen botànic, el sistema de producció o la categoria de qualitat

    Efficiency and Sustainability of the Distributed Renewable Hybrid Power Systems Based on the Energy Internet, Blockchain Technology and Smart Contracts-Volume II

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    The climate changes that are becoming visible today are a challenge for the global research community. In this context, renewable energy sources, fuel cell systems, and other energy generating sources must be optimally combined and connected to the grid system using advanced energy transaction methods. As this reprint presents the latest solutions in the implementation of fuel cell and renewable energy in mobile and stationary applications, such as hybrid and microgrid power systems based on the Energy Internet, Blockchain technology, and smart contracts, we hope that they will be of interest to readers working in the related fields mentioned above

    Data journeys in the sciences

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    This is the final version. Available from Springer via the DOI in this record. This groundbreaking, open access volume analyses and compares data practices across several fields through the analysis of specific cases of data journeys. It brings together leading scholars in the philosophy, history and social studies of science to achieve two goals: tracking the travel of data across different spaces, times and domains of research practice; and documenting how such journeys affect the use of data as evidence and the knowledge being produced. The volume captures the opportunities, challenges and concerns involved in making data move from the sites in which they are originally produced to sites where they can be integrated with other data, analysed and re-used for a variety of purposes. The in-depth study of data journeys provides the necessary ground to examine disciplinary, geographical and historical differences and similarities in data management, processing and interpretation, thus identifying the key conditions of possibility for the widespread data sharing associated with Big and Open Data. The chapters are ordered in sections that broadly correspond to different stages of the journeys of data, from their generation to the legitimisation of their use for specific purposes. Additionally, the preface to the volume provides a variety of alternative “roadmaps” aimed to serve the different interests and entry points of readers; and the introduction provides a substantive overview of what data journeys can teach about the methods and epistemology of research.European CommissionAustralian Research CouncilAlan Turing Institut

    Jornadas Nacionales de Investigación en Ciberseguridad: actas de las VIII Jornadas Nacionales de Investigación en ciberseguridad: Vigo, 21 a 23 de junio de 2023

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    Jornadas Nacionales de Investigación en Ciberseguridad (8ª. 2023. Vigo)atlanTTicAMTEGA: Axencia para a modernización tecnolóxica de GaliciaINCIBE: Instituto Nacional de Cibersegurida

    Differential evolution of non-coding DNA across eukaryotes and its close relationship with complex multicellularity on Earth

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    Here, I elaborate on the hypothesis that complex multicellularity (CM, sensu Knoll) is a major evolutionary transition (sensu Szathmary), which has convergently evolved a few times in Eukarya only: within red and brown algae, plants, animals, and fungi. Paradoxically, CM seems to correlate with the expansion of non-coding DNA (ncDNA) in the genome rather than with genome size or the total number of genes. Thus, I investigated the correlation between genome and organismal complexities across 461 eukaryotes under a phylogenetically controlled framework. To that end, I introduce the first formal definitions and criteria to distinguish ‘unicellularity’, ‘simple’ (SM) and ‘complex’ multicellularity. Rather than using the limited available estimations of unique cell types, the 461 species were classified according to our criteria by reviewing their life cycle and body plan development from literature. Then, I investigated the evolutionary association between genome size and 35 genome-wide features (introns and exons from protein-coding genes, repeats and intergenic regions) describing the coding and ncDNA complexities of the 461 genomes. To that end, I developed ‘GenomeContent’, a program that systematically retrieves massive multidimensional datasets from gene annotations and calculates over 100 genome-wide statistics. R-scripts coupled to parallel computing were created to calculate >260,000 phylogenetic controlled pairwise correlations. As previously reported, both repetitive and non-repetitive DNA are found to be scaling strongly and positively with genome size across most eukaryotic lineages. Contrasting previous studies, I demonstrate that changes in the length and repeat composition of introns are only weakly or moderately associated with changes in genome size at the global phylogenetic scale, while changes in intron abundance (within and across genes) are either not or only very weakly associated with changes in genome size. Our evolutionary correlations are robust to: different phylogenetic regression methods, uncertainties in the tree of eukaryotes, variations in genome size estimates, and randomly reduced datasets. Then, I investigated the correlation between the 35 genome-wide features and the cellular complexity of the 461 eukaryotes with phylogenetic Principal Component Analyses. Our results endorse a genetic distinction between SM and CM in Archaeplastida and Metazoa, but not so clearly in Fungi. Remarkably, complex multicellular organisms and their closest ancestral relatives are characterized by high intron-richness, regardless of genome size. Finally, I argue why and how a vast expansion of non-coding RNA (ncRNA) regulators rather than of novel protein regulators can promote the emergence of CM in Eukarya. As a proof of concept, I co-developed a novel ‘ceRNA-motif pipeline’ for the prediction of “competing endogenous” ncRNAs (ceRNAs) that regulate microRNAs in plants. We identified three candidate ceRNAs motifs: MIM166, MIM171 and MIM159/319, which were found to be conserved across land plants and be potentially involved in diverse developmental processes and stress responses. Collectively, the findings of this dissertation support our hypothesis that CM on Earth is a major evolutionary transition promoted by the expansion of two major ncDNA classes, introns and regulatory ncRNAs, which might have boosted the irreversible commitment of cell types in certain lineages by canalizing the timing and kinetics of the eukaryotic transcriptome.:Cover page Abstract Acknowledgements Index 1. The structure of this thesis 1.1. Structure of this PhD dissertation 1.2. Publications of this PhD dissertation 1.3. Computational infrastructure and resources 1.4. Disclosure of financial support and information use 1.5. Acknowledgements 1.6. Author contributions and use of impersonal and personal pronouns 2. Biological background 2.1. The complexity of the eukaryotic genome 2.2. The problem of counting and defining “genes” in eukaryotes 2.3. The “function” concept for genes and “dark matter” 2.4. Increases of organismal complexity on Earth through multicellularity 2.5. Multicellularity is a “fitness transition” in individuality 2.6. The complexity of cell differentiation in multicellularity 3. Technical background 3.1. The Phylogenetic Comparative Method (PCM) 3.2. RNA secondary structure prediction 3.3. Some standards for genome and gene annotation 4. What is in a eukaryotic genome? GenomeContent provides a good answer 4.1. Background 4.2. Motivation: an interoperable tool for data retrieval of gene annotations 4.3. Methods 4.4. Results 4.5. Discussion 5. The evolutionary correlation between genome size and ncDNA 5.1. Background 5.2. Motivation: estimating the relationship between genome size and ncDNA 5.3. Methods 5.4. Results 5.5. Discussion 6. The relationship between non-coding DNA and Complex Multicellularity 6.1. Background 6.2. Motivation: How to define and measure complex multicellularity across eukaryotes? 6.3. Methods 6.4. Results 6.5. Discussion 7. The ceRNA motif pipeline: regulation of microRNAs by target mimics 7.1. Background 7.2. A revisited protocol for the computational analysis of Target Mimics 7.3. Motivation: a novel pipeline for ceRNA motif discovery 7.4. Methods 7.5. Results 7.6. Discussion 8. Conclusions and outlook 8.1. Contributions and lessons for the bioinformatics of large-scale comparative analyses 8.2. Intron features are evolutionarily decoupled among themselves and from genome size throughout Eukarya 8.3. “Complex multicellularity” is a major evolutionary transition 8.4. Role of RNA throughout the evolution of life and complex multicellularity on Earth 9. Supplementary Data Bibliography Curriculum Scientiae Selbständigkeitserklärung (declaration of authorship

    Antimicrobial Peptides Aka Host Defense Peptides – From Basic Research to Therapy

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    This Special Issue reprint will address the most current and innovative developments in the field of HDP research across a range of topics, such as structure and function analysis, modes of action, anti-microbial effects, cell and animal model systems, the discovery of novel host-defense peptides, and drug development

    LIPIcs, Volume 274, ESA 2023, Complete Volume

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    LIPIcs, Volume 274, ESA 2023, Complete Volum
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