Scientific and Technical Contribution to the Development of an Overall Health Strategy in the Area of GMOs

The present report is the outcome of Project "Scientific and technical contribution to the development of an overall health strategy in the area of GMOs" carried out by the JRC-IHCP Biotechnology & GMOs Unit in the frame of study contract CT 30249, requested by the European Parliament Committee on Industry, Research and Energy. The study provides current knowledge on the issue and up-to-date opinions of experts on the potential short, medium and long term health impact associated with the consumption of GMOs. In addition, it contains the outcome of a research component that lead to the development of a multi-target analytical tool for the simultaneous identification of 39 GMOs.JRC.I.6-Biotechnology and GMO

The analysis of food samples for the presence of Genetically Modified Organisms - User Manual

The User Manual - background information and didactical guide for the participants attending the training courses on ‘The analysis of Food Samples for the Presence of Genetically Modified Organisms’ organised by the Joint Reseach Centre - provides the theoretical and detaied practical information on the methodologies and protocols for GMO detection used during the training. Structured in 12 Sessions, it covers a wide variety of techniques for the detection, identification, characterisation, and quantification of GMO.JRC.F.7-Knowledge for Health and Consumer Safet

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

Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota

Background: In previous studies we have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth, and it is influenced by the administration of specific antibiotics. These observations are compatible with a 'bacteriophage-like' behaviour of SARS-CoV-2. Methods: We have further elaborated on these unusual findings and here we present the results of three different supplementary experiments: (1) an electron-microscope analysis of samples of bacteria obtained from a faecal sample of a subject positive to SARS-CoV-2; (2) mass spectrometric analysis of these cultures to assess the eventual de novo synthesis of SARS-CoV-2 spike protein; (3) sequencing of SARS-CoV-2 collected from plaques obtained from two different gut microbial bacteria inoculated with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Results: Immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirmed presence of SARS-CoV-2 both outside and inside bacteria. De novo synthesis of SARS-CoV-2 spike protein was observed, as evidence that SARS-CoV-2 RNA is translated in the bacterial cultures. In addition, phage-like plaques were spotted on faecal bacteria cultures after inoculation with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Bioinformatic analyses on the reads obtained by sequencing RNA extracted from the plaques revealed nucleic acid polymorphisms, suggesting different replication environment in the two bacterial cultures. Conclusions: Based on these results we conclude that, in addition to its well-documented interactions with eukaryotic cells, SARS-CoV-2 may act as a bacteriophage when interacting with at least two bacterial species known to be present in the human microbiota. If the hypothesis proposed, i.e., that under certain conditions SARS-CoV-2 may multiply at the expense of human gut bacteria, is further substantiated, it would drastically change the model of acting and infecting of SARS-CoV-2, and most likely that of other human pathogenic viruses

Overview of EU National Legislation on Genomics

With the advent of fast, high efficiency and low cost DNA sequencing techniques, the ability to study the human genome by reading the sequence of its DNA is growing exponentially, with a resulting tremendous impact on many fields of scientific research. The application of genomics inside routine healthcare is boosting preventive medicine practices and can lead to personalised treatments that can highly improve the healthcare services and patients' health, and in the same time provide a wealth of data for medical research. In parallel, this has also led to the spread of commercial opportunities to provide consumers with the possibility of sequencing their genomes in a way which is both appealing and affordable. These commercial offers, however, do not always ensure the security of the generated data. In addition, the accuracy and reliability of the offered findings are not homogenous, as there are no standards to guarantee that the quality of the outputs satisfies minimum requirements - in fact, no agreements yet exist on the definition of these requirements. In this frame, a comprehensive knowledge of what is present at the legislative level in the member states of the European Union (plus Switzerland, Iceland and Norway) regarding the regulatory oversight of genomics technologies is of fundamental importance to frame the status of existing European norms, to understand whether possible incompatibilities might arise between frameworks and to highlight eventual gaps.JRC.F.7-Knowledge for Health and Consumer Safet

The Human Gut Microbiota: Overview and analysis of the current scientific knowledge and possible impact on healthcare and well-being

Recent years have seen a fast increase in the analytical capacity to read genetic information and in the ability to understand the link between the genetic information and the functioning of organisms. This has increased the scientific knowledge in previously underexploited fields. One example is the human microbiota and the understanding of the vital role that the microbiota plays in the physiological and psychological human health status and well-being. Brain degenerative diseases like Alzheimer and Parkinson are, for example, now considered to be linked to abnormalities in the functioning of the human gut microbiota. This understanding may have revolutionary impact on (personal) healthcare but this promise has not yet been fully recognized by the general public or the policy community and for example today, microbiota-related policy interventions are mostly restricted to the marketing and health claims of possible probiotic foods and food supplements. As the JRC is holding the responsibility for the knowledge management of health-related scientific information for policy, we present and discuss here the most recent information available on the vital role of the human gut microbiota and the associated opportunities for human health and well-being. This report provides the state-of-the-art of scientific progress and details how we are only starting to learn its importance for human health, food and chemicals safety, as well as for our protection against environmental stressors. We also indicate why and how the human gut microbiota is going to have an impact on healthcare, nutrition and well-being and how this may change the way we assess the risks of the food, drugs and chemicals we are in contact with.JRC.F.7-Knowledge for Health and Consumer Safet

Possible implications for SARS-CoV-2 impact on brain development

Funding Information: The authors would like to thank Dr. Marc Peschanski (I-Stem, Évry, France) for providing IMR90-hiPSCs, and Dr. Anna Navarro Cuenca for providing the license for the use of BioRender.com. Publisher Copyright: © 2022The possible neurodevelopmental consequences of SARS-CoV-2 infection are presently unknown. In utero exposure to SARS-CoV-2 has been hypothesized to affect the developing brain, possibly disrupting neurodevelopment of children. Spike protein interactors, such as ACE2, have been found expressed in the fetal brain, and could play a role in potential SARS-CoV-2 fetal brain pathogenesis. Apart from the possible direct involvement of SARS-CoV-2 or its specific viral components in the occurrence of neurological and neurodevelopmental manifestations, we recently reported the presence of toxin-like peptides in plasma, urine and fecal samples specifically from COVID-19 patients. In this study, we investigated the possible neurotoxic effects elicited upon 72-hour exposure to human relevant levels of recombinant spike protein, toxin-like peptides found in COVID-19 patients, as well as a combination of both in 3D human iPSC-derived neural stem cells differentiated for either 2 weeks (short-term) or 8 weeks (long-term, 2 weeks in suspension + 6 weeks on MEA) towards neurons/glia. Whole transcriptome and qPCR analysis revealed that spike protein and toxin-like peptides at non-cytotoxic concentrations differentially perturb the expression of SPHK1, ELN, GASK1B, HEY1, UTS2, ACE2 and some neuronal-, glia- and NSC-related genes critical during brain development. Additionally, exposure to spike protein caused a decrease of spontaneous electrical activity after two days in long-term differentiated cultures. The perturbations of these neurodevelopmental endpoints are discussed in the context of recent knowledge about the key events described in Adverse Outcome Pathways relevant to COVID-19, gathered in the context of the CIAO project (https://www.ciao-covid.net/).publishersversionpublishe

Rol del Joint Research Center y el Laboratorio de Referencia Comunitario (CRL-GMFF) en la Implementacion de la Normativa Europea

The lecture will provide an overview of available approaches and methods suitable for the purpose of GMO detection, identification and quantification. The lecture will include theoretical concepts of PCR - both qualitative and quantitative real-time - and the specific requirements for their application in GMO analysis. Practical aspects will also be covered: how to search for GMOs? What to search for? Screening versus event-specific protocols, proper choice of primers and PCR format according to specific needs and legislative requirements. In presenting principles, limits and possibilities of currently available analytical tools for the purpose of GMO detection, identification and quantification, the general context will be also presented: for example: aspects to be taken into consideration before starting activities in the field of GMO analysis, requirements for proper lab implementation, importance of samples and DNA quality, minimal (or optimal) requirements for the correct conduction of the work. The lecture will also include: meaning and importance of Certified Reference Materials, proficiency-testing schemes, GLP and accreditation, etc.; the importance of method validation will also be highlighted.JRC.I.6-Biotechnology and GMO

From Sampling to Quantification: Developments and Harmonization of Procedures for GMO Testing in the European Union

Objective of this chapter is to provide an overview of the scientific background and of the legal context defining the framework of genetically modified organism (GMO) testing across Europe. Specifically, we provide a comprehensive summary of the procedures for GMO testing, starting from sampling to final quantification of GMO content, including an overview of the legislative frame regulating such procedures and a summary of the actions taken at the European level to ensure harmonization of GMO testing among Member States. Some topics that have been object of scientific debates over the past years will be carefully addressed and the results of the scientific experience gained reported. Not all the issues raised found yet clear and complete answers; however, if on one hand remarkable progress has been made, allowing reaching commonly agreed definitions and applicative procedures, on the other some aspects are still under discussion, making the GMO issue an ongoing, interesting and still evolving topic.JRC.I.6-Biotechnology and GMO