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An In Vitro Dosimetry Tool for the Numerical Transport Modeling of Engineered Nanomaterials Powered by the Enalos RiskGONE Cloud Platform.

ABSTRACT: A freely available "in vitro dosimetry" web application is presented enabling users to predict the concentration of nanomaterials reaching the cell surface, and therefore available for attachment and internalization, from initial dispersion concentrations. The web application is based on the distorted grid (DG) model for the dispersion of engineered nanoparticles (NPs) in culture medium used for in vitro cellular experiments, in accordance with previously published protocols for cellular dosimetry determination. A series of in vitro experiments for six different NPs, with Ag and Au cores, are performed to demonstrate the convenience of the web application for calculation of exposure concentrations of NPs. Our results show that the exposure concentrations at the cell surface can be more than 30 times higher compared to the nominal or dispersed concentrations, depending on the NPs' properties and their behavior in the cell culture medium. Therefore, the importance of calculating the exposure concentration at the bottom of the cell culture wells used for in vitro arrays, i.e., the particle concentration at the cell surface, is clearly presented, and the tool introduced here allows users easy access to such calculations. Widespread application of this web tool will increase the reliability of subsequent toxicity data, allowing improved correlation of the real exposure concentration with the observed toxicity, enabling the hazard potentials of different NPs to be compared on a more robust basis.

SUBMITTER: Cheimarios N

PROVIDER: S-EPMC9697428 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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An In Vitro Dosimetry Tool for the Numerical Transport Modeling of Engineered Nanomaterials Powered by the Enalos RiskGONE Cloud Platform.

Cheimarios Nikolaos N Pem Barbara B Tsoumanis Andreas A Ilić Krunoslav K Vrček Ivana Vinković IV Melagraki Georgia G Bitounis Dimitrios D Isigonis Panagiotis P Dusinska Maria M Lynch Iseult I Demokritou Philip P Afantitis Antreas A

Nanomaterials (Basel, Switzerland) 20221108 22

A freely available "in vitro dosimetry" web application is presented enabling users to predict the concentration of nanomaterials reaching the cell surface, and therefore available for attachment and internalization, from initial dispersion concentrations. The web application is based on the distorted grid (DG) model for the dispersion of engineered nanoparticles (NPs) in culture medium used for in vitro cellular experiments, in accordance with previously published protocols for cellular dosimet ...[more]

PMID: 36432221

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Project description:BackgroundThere is a great need for screening tools capable of rapidly assessing nanomaterial toxicity. One impediment to the development of reliable in vitro screening methods is the need for accurate measures of cellular dose. We present here a methodology that enables accurate determination of delivered to cell dose metrics. This methodology includes (1) standardization of engineered nanomaterial (ENM) suspension preparation; (2) measurement of ENM characteristics controlling delivery to cells in culture; and (3) calculation of delivered dose as a function of exposure time using the ISDD model. The approach is validated against experimentally measured doses, and simplified analytical expressions for the delivered dose (Relevant In Vitro Dose (RID)f function) are derived for 20 ENMs. These functions can be used by nanotoxicologists to accurately calculate the total mass (RIDM), surface area (RIDSA), or particle number (RIDN) delivered to cells as a function of exposure time.ResultsThe proposed methodology was used to derive the effective density, agglomerate diameter and RID functions for 17 industrially-relevant metal and metal oxide ENMs, two carbonaceous nanoparticles, and non-agglomerating gold nanospheres, for two well plate configurations (96 and 384 well plates). For agglomerating ENMs, the measured effective density was on average 60% below the material density. We report great variability in delivered dose metrics, with some materials depositing within 24 hours while others require over 100 hours for delivery to cells. A neutron-activated tracer particle system was employed to validate the proposed in vitro dosimetry methodology for a number of ENMs (measured delivered to cell dose within 9% of estimated).ConclusionsOur findings confirm and extend experimental and computational evidence that agglomerate characteristics affect the dose delivered to cells. Therefore measurement of these characteristics is critical for effective use of in vitro systems for nanotoxicology. The mixed experimental/computational approach to cellular dosimetry proposed and validated here can be used by nanotoxicologists to accurately calculate the delivered to cell dose metrics for various ENMs and in vitro conditions as a function of exposure time. The RID functions and characterization data for widely used ENMs presented here can together be used by experimentalists to design and interpret toxicity studies.

Project description:BackgroundDecreasing costs make RNA sequencing technologies increasingly affordable for biologists. However, many researchers who can now afford sequencing lack access to resources necessary for downstream analysis. This means that even as algorithms to process RNA-Seq data improve, many biologists still struggle to manage the sheer volume of data produced by next generation sequencing (NGS) technologies. Scalable bioinformatics tools that exploit multiple platforms are needed to democratize bioinformatics resources in the sequencing era. This is essential for equipping many research groups in the life sciences with the tools to process the increasingly unwieldy datasets they produce.MethodsOne strategy to address this challenge is to develop a modern generation of sequence analysis tools capable of seamless data sharing and communication. Such tools will provide interoperability through offerings of interlinked resources. Systems of interlinked, scalable resources, which often incorporate cloud data storage, are broadly referred to as cyberinfrastructure. Cyberinfrastructure integrated tools will help researchers to robustly analyze large scale datasets by efficiently sharing data burdens across a distributed architecture. Additionally, interoperability will allow emerging tools to cross-adapt features of existing tools. It is important that these tools are designed to be easy to use for biologists.ResultsWe introduce fRNAkenseq, a powered-by-CyVerse RNA sequencing analysis tool that exhibits interoperability with other resources and meets the needs of biologists for comprehensive, easy to use RNA sequencing analysis. fRNAkenseq leverages a complex set of Application Programming Interfaces (APIs) associated with the NSF-funded cyberinfrastructure project, CyVerse, to execute FASTQ-to-differential expression RNA-Seq analyses. Integrating across bioinformatics platforms, fRNAkenseq also exploits cloud integration and cross-talk with another CyVerse associated tool, CoGe. fRNAkenseq offers novel features for the biologist such as more robust and comprehensive pipelines for enrichment than those currently available by default in a single tool, whether they are cloud-based or local installation. Importantly, cross-talk with CoGe allows fRNAkenseq users to execute RNA-Seq pipelines on an inventory of 47,000 archived genomes stored in CoGe or upload their own draft genome.

Dataset Information

An In Vitro Dosimetry Tool for the Numerical Transport Modeling of Engineered Nanomaterials Powered by the Enalos RiskGONE Cloud Platform.

Publications

An In Vitro Dosimetry Tool for the Numerical Transport Modeling of Engineered Nanomaterials Powered by the Enalos RiskGONE Cloud Platform.

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