A computational view on nanomaterial intrinsic and extrinsic features for nanosafety and sustainability

In recent years, an increasing number of diverse Engineered Nano-Materials (ENMs), such as nanoparticles and nanotubes, have been included in many technological applications and consumer products. The desirable and unique properties of ENMs are accompanied by potential hazards whose impacts are difficult to predict either qualitatively or in a quantitative and predictive manner. Alongside established methods for experimental and computational characterisation, physics-based modelling tools like molecular dynamics are increasingly considered in Safe and Sustainability-by-design (SSbD) strategies that put user health and environmental impact at the centre of the design and development of new products. Hence, the further development of such tools can support safe and sustainable innovation and its regulation. This paper stems from a community effort and presents the outcome of a four-year-long discussion on the benefits, capabilities and limitations of adopting physics-based modelling for computing suitable features of nanomaterials that can be used for toxicity assessment of nanomaterials in combination with data-based models and experimental assessment of toxicity endpoints. We review modern multiscale physics-based models that generate advanced system-dependent (intrinsic) or timeand environment-dependent (extrinsic) descriptors/features of ENMs (primarily, but not limited to nanoparticles, NPs), with the former being related to the bare NPs and the latter to their dynamic fingerprinting upon entering biological media. The focus is on (i) effectively representing all nanoparticle attributes for multicomponent nanomaterials, (ii) generation and inclusion of intrinsic nanoform properties, (iii) inclusion of selected extrinsic properties, (iv) the necessity of considering distributions of structural advanced features rather than only averages. This review enables us to identify and highlight a number of key challenges associated with ENMs’ data generation, curation, representation and use within machine learning or other advanced data-driven models to ultimately enhance toxicity assessment. Finally, the set up of dedicated databases as well as the development of grouping and read-across strategies based on the mode of action of ENMs using omics methods are identified as emerging methodologies for safety assessment and reduction of animal testing

Evidence-based activism: Patients' organisations, users' and activist's groups in knowledge

This article proposes the notion of ‘evidence-based activism’ to capture patients’ and health activists’ groups’ focus on knowledge production and knowledge mobilisation in the governance of health issues. It introduces empirical data and analysis on groups active in four countries (France, Ireland, Portugal and the United Kingdom), and in four condition-areas (rare diseases, Alzheimer’s disease, ADHD – Attention Deficit Hyperactivity Disorder and childbirth). It shows how these groups engage with, and articulate a variety of credentialed knowledge and ‘experiential knowledge’ with a view to explore concerned people’s situations, to make themselves part and parcel of the networks of expertise on their conditions in their national contexts, and to elaborate evidence on the issues they deem important to address both at an individual and at a collective level. This article argues that in contrast to health movements which contest institutions from the outside, patients’ and activists’ groups which embrace ‘evidence-based activism’ work ‘from within’ to imagine new epistemic and political appraisal of their causes and conditions. ‘Evidence-based activism’ entails a collective inquiry associating patients/activists and specialists/professionals in the conjoint fabrics of scientific statements and political claims. From a conceptual standpoint, ‘evidence-based activism’ sheds light on the ongoing co-production of matters of fact and matters of concern in contemporary technological democracies

The Movement of Research from the Laboratory to the Living Room: a Case Study of Public Engagement with Cognitive Science

Media reporting of science has consequences for public debates on the ethics of research. Accordingly, it is crucial to understand how the sciences of the brain and the mind are covered in the media, and how coverage is received and negotiated. The authors report here their sociological findings from a case study of media coverage and associated reader comments of an article (‘Does bilingualism influence cognitive aging?’) from Annals of Neurology. The media attention attracted by the article was high for cognitive science; further, as associates/members of the Centre where it was produced, the authors of the research reported here had rare insight into how the scientists responsible for the Annals of Neurology article interacted with the media. The data corpus included 37 news items and 228 readers’ comments, examined via qualitative thematic analysis. Media coverage of the article was largely accurate, without merely copying the press release. Analysis of reader comments showed these to be an important resource for considering issues of import to neuroethics scholars, as well as to scientists themselves (including how science communication shapes and is shaped by ethical, epistemic, and popular discourse). In particular, the findings demonstrate how personal experiences were vital in shaping readers’ accounts of their (dis)agreements with the scientific article. Furthermore, the data show how scientific research can catalyse political discussions in ways likely unanticipated by scientists. The analysis indicates the importance of dialogue between journalists, laboratory scientists and social scientists in order to support the communication of the messages researchers intend

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Influenza A Virus Induces Autophagosomal Targeting of Ribosomal Proteins

Seasonal epidemics of influenza A virus are a major cause of severe illness and are of high socio-economic relevance. For the design of effective antiviral therapies, a detailed knowledge of pathways perturbed by virus infection is critical. We performed comprehensive expression and organellar proteomics experiments to study the cellular consequences of influenza A virus infection using three human epithelial cell lines derived from human lung carcinomas: A549, Calu-1 and NCI-H1299. As a common response, the type I interferon pathway was up-regulated upon infection. Interestingly, influenza A virus infection led to numerous cell line-specific responses affecting both protein abundance as well as subcellular localization. In A549 cells, the vesicular compartment appeared expanded after virus infection. The composition of autophagsomes was altered by targeting of ribosomes, viral mRNA and proteins to these double membrane vesicles. Thus, autophagy may support viral protein translation by promoting the clustering of the respective molecular machinery in autophagosomes in a cell line-dependent manner