Knowledge and Instance Mapping: architecture for premeditated interoperability of disparate data for materials.

Predicting and elucidating the impacts of materials on human health and the environment is an unending task that has taken on special significance in the context of nanomaterials research over the last two decades. The properties of materials in environmental and physiological media are dynamic, reflecting the complex interactions between materials and these media. This dynamic behavior requires special consideration in the design of databases and data curation that allow for subsequent comparability and interrogation of the data from potentially diverse sources. We present two data processing methods that can be integrated into the experimental process to encourage pre-mediated interoperability of disparate material data: Knowledge Mapping and Instance Mapping. Originally developed as a framework for the NanoInformatics Knowledge Commons (NIKC) database, this architecture and associated methods can be used independently of the NIKC and applied across multiple subfields of nanotechnology and material science.

Bringing sex toys out of the dark: exploring unmitigated risks.

A majority of American adults report having used sex toys, which, by design, interact with intimate and permeable body parts yet have not been subject to sufficient risk assessment or management. Physical and chemical data are presented examining potential risks associated with four types of currently available sex toys: anal toy, beads, dual vibrator, and external vibrator. A standardized abrasion machine made real-time breakdown of products into microplastics and nanoplastics. The microplastics from the sex toys were then solvent extracted and analyzed using GC-MS. Rates of microplastics and nanoplastics released during abrasion testing from most microplastic release to least was the anal toy, beads, dual vibrator, external vibrator. Both micro- and nanoplastics particles were generated following the abrasion test, with the 50 percentile diameters (D50) ranging from the anal beads at 658.5 µm, dual vibrator at 887.83 µm, anal toy at 950 µm, and external vibrator at 1673.33 µm. The material matrix of each product was analyzed using ATR-FTIR, with results identifying the anal toy as polyethylene terephthalate (PET), the anal beads as polyvinyl chloride (PVC), the external vibrator as a silicone blend (polydimethylsiloxane [PDMS]), and the dual vibrator as a rubber mixture (polyisoprene). After extraction, phthalates known to be endocrine disruptors were present in all tested sex toys at levels exceeding hazard warnings. Analogous findings have been reported for similar materials that, when incorporated into other product categories, are subject to regulatory scrutiny in both the US and EU. This data set is not intended to be representative of sex toys as an entire class of products, nor are the abrasion experiments claiming to simulate exact use conditions. However, these exploratory data frame potential concerns, highlighting research questions and the need for prompt prioritization of protective action. Therefore, future studies and multi-stakeholder action are needed to understand and reduce risk for this class of products. Supplementary Information: The online version contains supplementary material available at 10.1186/s43591-023-00054-6.

The NanoInformatics Knowledge Commons: Capturing spatial and temporal nanomaterial transformations in diverse systems.

The empirical necessity for integrating informatics throughout the experimental process has become a focal point of the nano-community as we work in parallel to converge efforts for making nano-data reproducible and accessible. The NanoInformatics Knowledge Commons (NIKC) Database was designed to capture the complex relationship between nanomaterials and their environments over time in the concept of an 'Instance'. Our Instance Organizational Structure (IOS) was built to record metadata on nanomaterial transformations in an organizational structure permitting readily accessible data for broader scientific inquiry. By transforming published and on-going data into the IOS we are able to tell the full transformational journey of a nanomaterial within its experimental life cycle. The IOS structure has prepared curated data to be fully analyzed to uncover relationships between observable phenomenon and medium or nanomaterial characteristics. Essential to building the NIKC database and associated applications was incorporating the researcher's needs into every level of development. We started by centering the research question, the query, and the necessary data needed to support the question and query. The process used to create nanoinformatic tools informs usability and analytical capability. In this paper we present the NIKC database, our developmental process, and its curated contents. We also present the Collaboration Tool which was built to foster building new collaboration teams. Through these efforts we aim to: 1) elucidate the general principles that determine nanomaterial behavior in the environment; 2) identify metadata necessary to predict exposure potential and bio-uptake; and 3) identify key characterization assays that predict outcomes of interest.

Role of an active site loop in the promiscuous activities of Amycolatopsis sp. T-1-60 NSAR/OSBS.

The o-succinylbenzoate synthase (OSBS) family is part of the functionally diverse enolase superfamily. Many proteins in one branch of the OSBS family catalyze both OSBS and N-succinylamino acid racemization in the same active site. In some promiscuous NSAR/OSBS enzymes, NSAR activity is biologically significant in addition to or instead of OSBS activity. Identifying important residues for each reaction could provide insight into how proteins evolve new functions. We have made a series of mutations in Amycolatopsis sp. T-1-60 NSAR/OSBS in an active site loop, referred to as the 20s loop. This loop affects substrate specificity in many members of the enolase superfamily but is poorly conserved within the OSBS family. Deletion of this loop decreased OSBS and NSAR catalytic efficiency by 4500-fold and 25,000-fold, respectively, showing that it is essential. Most point mutations had small effects, changing the efficiency of both NSAR and OSBS activities <10-fold compared to that of the wild type. An exception was F19A, which reduced kcat/KM(OSBS) 200-fold and kcat/KM(NSAR) 120-fold. Mutating the surface residue R20E, which can form a salt bridge to help close the 20s loop over the active site, had a more modest effect, decreasing kcat/KM of OSBS and NSAR reactions 32- and 8-fold, respectively. Several mutations increased KM of the NSAR reaction more than that of the OSBS reaction. Thus, both activities require the 20s loop, but differences in how mutations affect OSBS and NSAR activities suggest that some substitutions in this loop made a small contribution to the evolution of NSAR activity, although additional mutations were probably required.