Search

OnTuesday, 9th Nov 2021, the NanoCommons team, in a joint initiative with the NanoSafety Cluster, offered an online webinar on the use of their Nanoinformatics data services & toolsaccessible via the NanoCommons Infrastructure and Knowledge Base (NC KB). Hosts: Christine Balmer, UKCEH, UK, Beatriz Alfaro-Serrano, BNN, AT, Martin Himly, PLUS, AT, Chair of NanoSafety Cluster WG-A on Education, Training, and Communication The H2020 research e-infrastructure projectNanoCommonsis fostering collaborative research by trying to bring the nanosafety community together to work hands-on on the establishment of ways to make data and software platforms, developed in the different projects, to talk to each other. In order to give this a major push, we organised a workshop where, first, different organisations, that have already applied for Transnational Access (TA) projects with NanoCommons, reported about their experiences. This was followed by presentations on how the learnings from these projects resulted in collaboration and interoperability concepts, which could be extended to span across different tools and platforms, and on the upcoming training activities of NanoCommons and other possible follow-ups to this workshop. This workshop showcased how NanoCommons could support all of you, individually and as a group, as independent data harmoniser, platform harmoniser (e.g. through joint APIs, containerisation solutions, etc.) and overall data/metadata consultant not creating new tools or replacing existing solutions but to bring all these closer together so that they can be combined into integrated workflows. This could be based on common metadata and data standards, linking of data warehouses, workflow tools (KNIME, Jupyter) and deployment options to combine different services with complementary features. This could also be supplemented by ways of collaborative dissemination of the results from the projects and knowledge sharing like common service catalogues, training and knowledge platforms and the shared usage of applications like electronic lab notebooks. These are just some first thought-starters but of course we are open to hearing your needs and even more important things you could / would like to bring in. Attached here you find the pdf of the entire webinar slide set. The webinar recording is amongst others available online at the NanoCommons YouTube channel, for a direct link to the recordings of this event click here. Furthermore, you find additional information on related trainings at the NanoCommons Infrastructure, in the NanoCommons Customer Guidance Handbook, and at the ELIXIR TeSS channel of NanoCommons.

Nanomaterials have found extensive interest in the development of novel vaccines, as adjuvants and/or carriers in vaccination platforms. Conjugation of protein antigens at the particle surface by non-covalent adsorption is the most widely used approach in licensed particulate vaccines. Hence, it is essential to understand proteins’ structural integrity at the material interface in order to develop safe-by-design nanovaccines. In this study, we utilized two model proteins, the wild-type allergen Bet v 1 and its hypoallergenic fold variant (BM4), to compare SiO2 nanoparticles with Alhydrogel® as particulate systems. A set of biophysical and functional assays including circular dichroism spectroscopy and proteolytic degradation was used to examine the antigens’ structural integrity at the material interface. Conjugation of both biomolecules to the particulate systems decreased their proteolytic stability. However, we observed qualitative and quantitative differences in antigen processing concomitant with differences in their fold stability. These changes further led to an alteration in IgE epitope recognition. Here, we propose a toolbox of biophysical and functional in vitro assays for the suitability assessment of nanomaterials in the early stages of vaccine development. These tools will aid in safe-by-design innovations and allow fine-tuning the properties of nanoparticle candidates to shape a specific immune response.

Iron oxide nanoparticles (IONPs) bear big hopes in nanomedicine due to their (potential) applications in tumor therapy, drug delivery or bioimaging. However, as foreign entities, such particles may be recognized by the immune system and, thus, lead to inflammation, hypersensitivity or anaphylactic shock. In addition, an overload with iron is known to cause oxidative stress. In this short review, we summarize the biological effects of such particles with a major focus on IONP-formulations used for bioimaging purposes and their effects on the human immune system. We conclude that especially the characteristics of the particles (size, shape, surface charge, coating, etc.) as well as the presence of bystander substances, such as bacterial endotoxin are important factors determining the resulting biological and immunological effects of IONPs. Further studies are needed in order to establish clear structure-activity relationships.

The innate immune system evolved to detect and react against potential dangers such as bacteria, viruses, and environmental particles. The advent of modern technology has exposed innate immune cells, such as monocytes, macrophages, and dendritic cells, to a relatively novel type of particulate matter, i.e., engineered nanoparticles. Nanoparticles are not inherently pathogenic, and yet cases have been described in which specific nanoparticle types can either induce innate/inflammatory responses or modulate the activity of activated innate cells. Many of these studies rely upon activation by agonists of toll-like receptors, such as lipopolysaccharide or peptidoglycan, instead of the more realistic stimulation by whole live organisms. In this review we examine and discuss the effects of nanoparticles on innate immune cells activated by live bacteria. We focus in particular on how nanoparticles may interfere with bacterial processes in the context of innate activation, and confine our scope to the effects due to particles themselves, rather than to molecules adsorbed on the particle surface. Finally, we examine the long-lasting consequences of coexposure to nanoparticles and bacteria, in terms of potential microbiome alterations and innate immune memory, and address nanoparticle-based vaccine strategies against bacterial infection.

The increasing prevalence of allergic diseases demands efficient therapeutic strategies for their mitigation. Allergen-specific immunotherapy (AIT) is the only causal rather than symptomatic treatment method available for allergy. Currently, AIT is being administered using immune response modifiers or adjuvants. Adjuvants aid in the induction of a vigorous and long-lasting immune response, thereby improving the efficiency of AIT. The successful development of a novel adjuvant requires a thorough understanding of the conventional and novel adjuvants under development. Thus, this review discusses the potentials and challenges of these adjuvants and their mechanism of action. Vaccine development based on nanoparticles is a promising strategy for AIT, due to their inherent physicochemical properties, along with their ease of production and ability to stimulate innate immunity. Although nanoparticles have provided promising results as an adjuvant for AIT in in vivo studies, a deeper insight into the interaction of nanoparticle–allergen complexes with the immune system is necessary. This review focuses on the methods of harnessing the adjuvant effect of nanoparticles by detailing the molecular mechanisms underlying the immune response, which includes allergen uptake, processing, presentation, and induction of T cell differentiation.

NanoCommons is a research e-infrastructure project offering access to high quality nanoinformatics tools and services for nanotechnology and nanosafety stakeholders (academia, industry, regulators). It is user-led, offering and developing the services needed by the user community of nanotechnology, nanosafety and related fields. NanoCommons is built on 3 main pillars: joint research activities, networking activities and transnational access services, covering four categories relevant for nanosafety assessment: experimental workflows design and implementation; data processing and analysis; data visualisation and predictive toxicity; data storage and online accessibility. These services are designed to promote data FAIRness (Findable, Accessible, Interoperable, and Reusable), a key NanoCommons goal, that can be made Open through the NanoCommons Knowledgebase. Thus, NanoCommons provides innovative solutions for data mining, harmonisation, utilisation and re-utilisation, including incorporation of a range of modelling and decision support tools that require and/or can produce organised, high-quality datasets. A number of online training tools have been developed for each of the offered services to help users chose and use the services relevant to their needs. The NanoCommons help-desk and training library shall bridge academic research with industry and regulators, as recommended by the EU NanoSafety Cluster‘s “Closer to the Market” Research Roadmap serving the Safe-by-Design concept in nanotechnology.

NanoCommons is a research e-infrastructure project offering access to high quality nanoinformatics services for nanosafety assessors in academia, industry, regulatory agencies. It is user-led, offering and developing the services needed by the user community of nanotechnology, nanosafety and related fields. NanoCommons is built on 3 main pillars: joint research activities, networking activities and transnational access services, covering four categories relevant for nanosafety assessment: experimental workflows design and implementation; data processing and analysis; data visualisation and predictive toxicity; data storage and online accessibility. These services are designed to promote data FAIRness (Findable, Accessible, Interoperable, and Reusable), a key NanoCommons goal, that can be made Open through the NanoCommons Knowledgebase. Thus, NanoCommons provides innovative solutions for data mining, harmonisation, utilisation and re-utilisation, including incorporation of a range of modelling and decision support tools that require and/or can produce organised, high-quality datasets. A number of online training tools have been developed for each of the offered services to help users chose the services relevant to their research questions and applications. The NanoCommons infrastructure encompassing a training library shall bridge academic research with industry and regulators, as recommended by the EU NanoSafety Cluster‘s “Closer to the Market” Research Roadmap serving the Safe-by-Design concept in nanotechnology., {"references":["https://www.openaire.eu/how-to-make-your-data-fair"]}

Additional file 1: Table S1. Upregulated polypeptides identified by mass spectrometry from A549 proteome in response to PLA-NP with their respective description.

Additional file 1. Transmission electron micrographs, hydrolysis plots, IR spectra and fitting results.

Additional file 8. Proteins bound to AuNP when using 100Â % FCS. The identity of unique proteins identified, via LTQ-Orbitrap mass spectrometry, in AuNP-FCS complexes were identified using http://www.uniprot.org (taxonomy: mammalia); evaluated when incubated in 100Â % FCS; data presented is of unique proteins identified in all 3 biological replicates; this analysis was performed with 3 technical replicates of each biological replicate; for confidence of identification the proteins presented in these graphs are only proteins found in every biological replicate.

Additional file 1. EELS measured at sites of electron dense particulate matter observed in micrographs. Intracellular particles are identified with red lines (A–F), extracellular particles with green lines (E–F), and particles observed during perceived exocytosis with red lines (G–H); Au = gold, Co = control, P = phosphorus.

Additional file 10. General pattern of AuNP-protein interactions â identity of unique proteins. The identity of unique proteins identified, via LTQ-Orbitrap mass spectrometry, in AuNP-FCS complexes were identified using http://www.uniprot.org (taxonomy: mammalia); evaluated when incubated in 10, 55, and 100Â % FCS; data presented is of unique proteins identified in every biological replicate and all 3 serum conditions.

Additional file 5. Immune response of THP-1 cells to NP solvents. Secretion of CCL2 (A-C), TNF-α (D-F), IL-6 (G-I) and IL-1ß (J-L) from PMA-stimulated cells, in response to sodium citrate (2.2 mM stock) or chitosan (0.1 % stock) at dilutions relevant to AuNP exposures; 1 ng/ml LPS was used for co-stimulation; with 1 and 100 ng/ml LPS for controls; results are expressed as cytokine release in pg/ml, R = 3, and each data point represents the mean ± SEM.

Additional file 7. Proteins bound to AuNP when using 55Â % FCS. The identity of unique proteins identified, via LTQ-Orbitrap mass spectrometry, in AuNP-FCS complexes were identified using http://www.uniprot.org (taxonomy: mammalia); evaluated when incubated in 55Â % FCS; data presented is of unique proteins identified in all 3 biological replicates; this analysis was performed with 3 technical replicates of each biological replicate; for confidence of identification the proteins presented in these graphs are only proteins found in every biological replicate.

Additional file 6. Proteins bound to AuNP when using 10Â % FCS. The identity of unique proteins identified, via LTQ-Orbitrap mass spectrometry, in AuNP-FCS complexes were identified using http://www.uniprot.org (taxonomy: mammalia); evaluated when incubated in 10Â % FCS; data presented is of unique proteins identified in all 3 biological replicates; this analysis was performed with 3 technical replicates of each biological replicate; for confidence of identification the proteins presented in these graphs are only proteins found in every biological replicate.

Additional file 4. AuNPs induced pro-inflammatory response of THP-1 cells in different cell activation states. IL-1β release from THP-1 cells in response to treatment with Au_CHIT-H (administered dose of 2.5 µg/ml) for 4 (A and C) or 24 h (B and D), in the presence and absence of 1 ng/ml LPS co-stimulation, and without (A-B) or with (C-D) PMA-priming. Results are expressed as IL-1β release (pg/ml), and each data point represents the mean ± SEM, R = 3. Statistical significance is shown by * = p

Additional file 3. Cytotoxicity assessment of NP solvents in THP-1 cells. Viability (mitochondrial activity) (A-C) and cytotoxicity (LDH release) (D-F) in PMA-stimulated cells, after treatment with sodium citrate (2.2 mM stock) or chitosan (0.1 % stock) at dilutions relevant to AuNP exposures, for 4, 24 and 48 h; 1 ng/ml LPS was used for co-stimulation, Triton X-100 was used as positive control. Results are expressed as fluorescence intensity for viability assays, and as absorbance for LDH release, R = 3, each data point represents the mean ± SEM.

Supplementary Material - Stoehr et al. PFT 2015. (PDF 838Â kb)

Additional file 9. General pattern of AuNP-protein interactions â number of unique proteins. The number of unique proteins identified, via LTQ-Orbitrap mass spectrometry, in AuNP-FCS complexes were identified using http://www.uniprot.orf (taxonomy: mammalia); evaluated when incubated in 10, 55, and 100Â % FCS; data presented is of unique proteins identified in every biological replicate and all 3 serum conditions.

Additional file 2. Au_CHIT-L induced cytotoxicity in THP-1 cells. Viability (mitochondrial activity) (A) and cytotoxicity (LDH release) (B) in PMA-stimulated cells, after treatment with Au_CHIT-L, for 24 and 48 h; 1 ng/ml LPS was used for co-stimulation, Triton X-100 was used as positive control. Results are expressed as, for viability, % viability compared to 100 % control cells, and as the ratio change compared to controls for LDH release, and each data point represents the mean ± SEM, R = 4; statistical significance (determined by ANOVA with Tukey posthoc) is shown by ^ = p

Additional file 2: Table S2. Downregulated polypeptides identified by mass spectrometry from A549 proteome in response to PLA-NP with their respective description.

Determination of conjugated allergen after the incubation in human plasma performed by Coomassie-stained SDS-PAGE (A-C) and Western blots (D-F). (TIF 526Â kb)

Additional file 2: Table S2. Downregulated polypeptides identified by mass spectrometry from A549 proteome in response to PLA-NP with their respective description.

Determination of conjugated allergen after the incubation in human plasma performed by Coomassie-stained SDS-PAGE (A-C) and Western blots (D-F). (TIF 526Â kb)

The rapid development of nanotechnologies and increased production and use of nanomaterials raise concerns about their potential toxic effects for human health and environment. To evaluate the biological effects of nanomaterials, a set of reliable and reproducible methods and development of standard operating procedures (SOPs) is required. In the framework of the European FP7 NanoValid project, three different cell viability assays (MTS, ATP content, and caspase-3/7 activity) with different readouts (absorbance, luminescence and fluorescence) and two immune assays (ELISA of pro-inflammatory cytokines IL1-β and TNF-α) were evaluated by inter-laboratory comparison. The aim was to determine the suitability and reliability of these assays for nanosafety assessment. Studies on silver and copper oxide nanoparticles (NPs) were performed, and SOPs for particle handling, cell culture, and in vitro assays were established or adapted. These SOPs give precise descriptions of assay procedures, cell culture/seeding conditions, NPs/positive control preparation and dilutions, experimental well plate preparation, and evaluation of NPs interference. The following conclusions can be highlighted from the pan-European inter-laboratory studies: Testing of NPs interference with the toxicity assays should always be conducted. Interference tests should be designed as close as possible to the cell exposure conditions. ATP and MTS assays gave consistent toxicity results with low inter-laboratory variability using Ag and CuO NPs and different cell lines and therefore, could be recommended for further validation and standardization. High inter-laboratory variability was observed for Caspase 3/7 assay and ELISA for IL1-β and TNF-α measurements., by Superb K. Misra et al.