Towards plant species identification in complex samples: a bioinformatics pipeline for the identification of novel nuclear barcode candidates

Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.JRC.I.3-Molecular Biology and Genomic

Enhancing fish species identification using novel markers and emerging technologies

Establishing an efficient traceability framework for fish products is crucial for consumer protection and fisheries management and conservation. This is well reflected in the EU legislation. The EU general food law emphasizes strongly that European citizens must have access to safe and wholesome food of the highest standard. Consumer protection is supported by a stringent traceability concept as stipulated in Regulation (EC) 178/2002. This notion is also expressed in the Common Fisheries Policy (CFP) basic regulation (EU) 1380/2013, according to which fishing and aquaculture must be environmentally, economically and socially sustainable while providing a source of healthy food for all EU citizens. Under the CFP the need for traceability is not exclusively raised in the context of consumer protection, but also as a necessary component for fisheries control and enforcement in Regulation (EU) 1224/2009 and in the context of the EU’s ambitious strategy to fight Illegal, Unreported and Unregulated (IUU) fishing under the remit of Regulation (EC) 1005/2008. Recent scientific advances, particularly in the fields of genetics and genomics, have led to the development of novel and improved technologies, and efforts are under way to harness their potential for the species identification of unknown fish samples or products. This report reviews these efforts, describing the technologies and the early results obtained for fish product traceability. Each of these technologies have the potential to fill some specific existing gaps, although they come with their own individual set of disadvantages. Understanding those and monitoring progress is thus crucial for their proper integration in existing traceability frameworks.JRC.F.7-Knowledge for Health and Consumer Safet

Nature-based strategies to regenerate the functioning and biodiversity of vineyards

16 páginas.- 2 figuras.- 1 Box.- 138 referenciasGrapevine is one of the most important perennial fruit crops worldwide. Historically, vineyards were compatible with soil conservation practices and multitrophic biodiversity, but vineyards are now generally eroded and biologically impoverished, making them more susceptible to pests and diseases. However, the idiosyncrasy of the wine sector places wine growers in a unique position to lead the adoption of a range of sustainable management strategies and, thus, to pioneer a wider transformation of the agricultural sector. In this article, we provide an overview of nature-based management strategies that may be used for the regeneration of the functioning and biodiversity of vineyards and that may also lead to improved plant nutrition, grape berry quality and the suppression of pathogens and pests. These strategies include the use of microbial and nonmicrobial biostimulants, fertilization with organic amendments as well as foliar fertilization with nature-based products, the use of cover crops and the reintegration of livestock in vineyards, especially sheep. We will also pay special attention to the implementation of circular economy in the vineyard in relation to the previously mentioned management strategies and will also discuss the importance of considering all these aspects from a holistic and integrative perspective, rather than taking them into account as single factors. Assuming the integral role of soils in the functioning of agroecosystems, soils will be considered transversally across all sections. Finally, we will argue that the time is now ripe for innovation from the public and private sectors to contribute to the sustainable management of vineyards while maintaining, or even improving, the profit margin for farmers and winemakers.This review article is, in part, the result of a workshop (I Jornadas ‘Suelos Vivos’ para la regeneración de la vida en suelos de viñedos gaditanos; https://suelosvivos.es/i-jornadas-suelos-vivos/) carried out within the context of the ‘Suelos Vivos’ Regional Operational Group of the EIP-Agri, which was celebrated between 23 and 24 March 2023 in Puerto Real, Cádiz. Raúl Ochoa-Hueso was supported by the Ramón y Cajal programme from the MICINN (RYC-2017 22032), by the Spanish Ministry of Science and Innovation for the I + D + i project PID2019-106004RA-I00 funded by MCIN/AEI/10.13039/501100011033, by the Fondo Europeo de Desarrollo Regional (FEDER) y la Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático ‘01 - Refuerzo de la investigación, el desarrollo tecnológico y la innovación’): P20_00323 (FUTUREVINES), and by the Fondo Europeo Agrícola de Desarrollo Rural (FEADER) through the ‘Ayudas a Grupos operativos de la Asociación Europea de Innovación (AEI) en materia de productividad y sostenibilidad agrícolas’, Referencia: GOPC-CA-20-0001. Manuel Delgado-Baquerizo acknowledges support from TED2021-130908B-C41/AEI/10.13039/501100011033/Unión Europea NextGenerationEU/PRTR and from the Spanish Ministry of Science and Innovation for the I + D + i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. Cristina Lazcano acknowledges support from the California Department of Food and Agriculture (21-0433-021-SF) and the Foundation for Food and Agriculture Research (FFAR, CA21-SS-0000000193). Lilia Serrano-Grijalva thanks the European Union's Horizon 2020 research and innovation programme who funded her work under the Marie Skłodowska-Curie Grant Agreement No. 890874Peer reviewe

Examining the immune signatures of SARS-CoV-2 infection in pregnancy and the impact on neurodevelopment: Protocol of the SIGNATURE longitudinal study.

The COVID-19 pandemic represents a valuable opportunity to carry out cohort studies that allow us to advance our knowledge on pathophysiological mechanisms of neuropsychiatric diseases. One of these opportunities is the study of the relationships between inflammation, brain development and an increased risk of suffering neuropsychiatric disorders. Based on the hypothesis that neuroinflammation during early stages of life is associated with neurodevelopmental disorders and confers a greater risk of developing neuropsychiatric disorders, we propose a cohort study of SARS-CoV-2-infected pregnant women and their newborns. The main objective of SIGNATURE project is to explore how the presence of prenatal SARS-CoV-2 infection and other non-infectious stressors generates an abnormal inflammatory activity in the newborn. The cohort of women during the COVID-19 pandemic will be psychological and biological monitored during their pregnancy, delivery, childbirth and postpartum. The biological information of the umbilical cord (foetus blood) and peripheral blood from the mother will be obtained after childbirth. These samples and the clinical characterisation of the cohort of mothers and newborns, are tremendously valuable at this time. This is a protocol report and no analyses have been conducted yet, being currently at, our study is in the recruitment process step. At the time of this publication, we have identified 1,060 SARS-CoV-2 infected mothers and all have already given birth. From the total of identified mothers, we have recruited 537 SARS-COV-2 infected women and all of them have completed the mental health assessment during pregnancy. We have collected biological samples from 119 mothers and babies. Additionally, we have recruited 390 non-infected pregnant women

CIBERER : Spanish national network for research on rare diseases: A highly productive collaborative initiative

Altres ajuts: Instituto de Salud Carlos III (ISCIII); Ministerio de Ciencia e Innovación.CIBER (Center for Biomedical Network Research; Centro de Investigación Biomédica En Red) is a public national consortium created in 2006 under the umbrella of the Spanish National Institute of Health Carlos III (ISCIII). This innovative research structure comprises 11 different specific areas dedicated to the main public health priorities in the National Health System. CIBERER, the thematic area of CIBER focused on rare diseases (RDs) currently consists of 75 research groups belonging to universities, research centers, and hospitals of the entire country. CIBERER's mission is to be a center prioritizing and favoring collaboration and cooperation between biomedical and clinical research groups, with special emphasis on the aspects of genetic, molecular, biochemical, and cellular research of RDs. This research is the basis for providing new tools for the diagnosis and therapy of low-prevalence diseases, in line with the International Rare Diseases Research Consortium (IRDiRC) objectives, thus favoring translational research between the scientific environment of the laboratory and the clinical setting of health centers. In this article, we intend to review CIBERER's 15-year journey and summarize the main results obtained in terms of internationalization, scientific production, contributions toward the discovery of new therapies and novel genes associated to diseases, cooperation with patients' associations and many other topics related to RD research

Examining the immune signatures of SARS-CoV-2 infection in pregnancy and the impact on neurodevelopment: Protocol of the SIGNATURE longitudinal study

The COVID-19 pandemic represents a valuable opportunity to carry out cohort studies that allow us to advance our knowledge on pathophysiological mechanisms of neuropsychiatric diseases. One of these opportunities is the study of the relationships between inflammation, brain development and an increased risk of suffering neuropsychiatric disorders. Based on the hypothesis that neuroinflammation during early stages of life is associated with neurodevelopmental disorders and confers a greater risk of developing neuropsychiatric disorders, we propose a cohort study of SARS-CoV-2-infected pregnant women and their newborns. The main objective of SIGNATURE project is to explore how the presence of prenatal SARS-CoV-2 infection and other non-infectious stressors generates an abnormal inflammatory activity in the newborn. The cohort of women during the COVID-19 pandemic will be psychological and biological monitored during their pregnancy, delivery, childbirth and postpartum. The biological information of the umbilical cord (foetus blood) and peripheral blood from the mother will be obtained after childbirth. These samples and the clinical characterisation of the cohort of mothers and newborns, are tremendously valuable at this time. This is a protocol report and no analyses have been conducted yet, being currently at, our study is in the recruitment process step. At the time of this publication, we have identified 1,060 SARS-CoV-2 infected mothers and all have already given birth. From the total of identified mothers, we have recruited 537 SARS-COV-2 infected women and all of them have completed the mental health assessment during pregnancy. We have collected biological samples from 119 mothers and babies. Additionally, we have recruited 390 non-infected pregnant women.This work has received support from the Fundación Alicia Koplowitz to realize the epigenetic wide association study and to the clinical assessment to the children. This work has also received public support from the Consejería de Salud y Familias para la financiación de la investigación, desarrollo e innovación (i + d + i) biomédica y en ciencias de la salud en Andalucía (CSyF 2021 - FEDER). Grant Grant number PECOVID- 0195-2020. Convocatoria financiada con Fondo Europeo de Desarrollo Regional (FEDER) al 80% dentro del Programa Operativo de Andalucía FEDER 2014-2020. Andalucía se mueve con Europa. NG-T received payment under Rio Hortega contract CM20-00015 with the Carlos III Health Institute.Peer reviewe

TableS1 of ML-based predictive gut microbiome analysis for health assessment

Complete list of species associated with the COVID and Control cohort (ANOVA F score > 1). Comparison with respect to the original set of species used by Gupta et al., and ANOVA-F values are reported.DECLARATION The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication

Memoria descriptiva del desembarque del material de cañones de 38,1 centímetros para la Batería de Las Cenizas (Portmán). Cartagena

La puntería a gran distancia de las piezas de largo alcance especialmente aplicada al tiro sobre tierra de las piezas de artillería de costa / Fernando Puertas Gallardo; El tiro de las baterías móviles en la defensa de costa / Ángel Calderón; Sunchado de cañones / Antonio Ramírez de Orellan

Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates

<div><p>Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.</p></div