Search Results (13)

DprA (also known as Smf) is a conserved RecA mediator originally characterized by its role in natural chromosomal transformation, yet its widespread presence across bacteria hints at broader DNA metabolic functions. Here, we demonstrate that Bacillus subtilis DprA enhances the frequency of Escherichia coli Hfr conjugation in vivo. In vitro, RecA·ATP binds and cooperatively polymerizes in a 50-nucleotide (nt) polydeoxy T (dT)₅₀ ssDNA to form dynamic filaments that SSB inhibits, an effect fully reversed by Bacillus subtilis DprA. Escherichia coli RecA bound to (dT)₂₁ exhibits minimal dATPase activity, but the addition of B. subtilis DprA significantly stimulates RecA dATP hydrolysis. B. subtilis RecA·dATP readily assembles on (dT)₂₀ complexes, and DprA allosterically activates RecA on even shorter (dT)₁₅ substrates. Combining biochemical assays with a fully atomic model of the RecA–DprA–ssDNA complex, we proposed that only one DNA binding site of the DprA dimer engages the ssDNA during RecA loading, owing to steric constraints. This work refines the mechanism of DprA-mediated RecA nucleation and defines the minimal ssDNA footprint required for mediator activity. Full article

This research explores Dynamic Probabilistic Risk Assessment (DPRA) using EMRALD to evaluate the reliability and safety of passive safety systems in nuclear reactors, with a focus on mitigating Loss of Coolant Accidents (LOCAs). The BWRX-300 Small Modular Reactor (SMR) is used as an example to illustrate the proposed DPRA methodology, which is broadly applicable for enhancing traditional Probabilistic Safety Assessment (PSA). Unlike static PSA, DPRA incorporates time-dependent interactions and system dynamics, allowing for a more realistic assessment of accident progression. EMRALD enables the modelling of system failures and interactions in real time using dynamic event trees and Monte Carlo simulations. This study identifies critical vulnerabilities in passive safety systems and quantifies the Core Damage Frequency (CDF) under LOCA scenarios. The findings demonstrate the advantages of DPRA over traditional PSA in capturing complex failure mechanisms and providing a more comprehensive and accurate risk assessment. The insights gained from this research contribute to improving passive safety system designs and enhancing nuclear reactor safety strategies for next-generation reactors. Full article

Skin sensitisation is a critical adverse effect assessed to ensure the safety of compounds and materials exposed to the skin. Alongside the development of new approach methodologies (NAMs), defined approaches (DAs) have been established to promote skin sensitisation potency assessment by adopting and integrating standardised in vitro, in chemico, and in silico methods with specified data analysis procedures to achieve reliable and reproducible predictions. The incorporation of additional NAMs could help increase accessibility and flexibility. Using superior algorithms may help improve the accuracy of hazard and potency assessment and build confidence in the results. Here, we introduce two new DA models, with the aim to build DAs on freely available software and the newly developed kDPRA for covalent binding of a chemical to skin peptides and proteins. The new DA models are built on an existing Bayesian network (BN) modelling approach and expand on it. The new DA models include kDPRA data as one of the in vitro parameters and utilise in silico inputs from open-source QSAR models. Both approaches perform at least on par with the existing BN DA and show 63% and 68% accuracy when predicting four LLNA potency classes, respectively. We demonstrate the value of the Bayesian network’s confidence indications for predictions, as they provide a measure for differentiating between highly accurate and reliable predictions (accuracies up to 87%) in contrast to low-reliability predictions associated with inaccurate predictions. Full article

Since 2020, the REACh regulation requires toxicological data on nanoforms of materials, including the assessment of their skin-sensitizing properties. Small molecules’ skin sensitization potential can be assessed by new approach methodologies (NAMs) addressing three key events (KE: protein interaction, activation of dendritic cells, and activation of keratinocytes) combined in a defined approach (DA) described in the OECD guideline 497. In the present study, the applicability of three NAMs (DPRA, LuSens, and h-CLAT) to nine materials (eight inorganic nanomaterials (NM) consisting of CeO₂, BaSO₄, TiO₂ or SiO₂, and quartz) was evaluated. The NAMs were technically applicable to NM using a specific sample preparation (NANOGENOTOX dispersion protocol) and method modifications to reduce interaction of NM with the photometric and flowcytometric read-outs. The results of the three assays were combined according to the defined approach described in the OECD guideline No. 497; two of the inorganic NM were identified as skin sensitizers. However, data from animal studies (for ZnO, also human data) indicate no skin sensitization potential. The remaining seven test substances were assessed as “inconclusive” because all inorganic NM were outside the domain of the DPRA, and the achievable test concentrations were not sufficiently high according to the current test guidelines of all three NAMs. The use of these NAMs for (inorganic) NM and the relevance of the results in general are challenged in three ways: (i) NAMs need modification to be applicable to insoluble, inorganic matter; (ii) current test guidelines lack adequate concentration metrics and top concentrations achievable for NM; and (iii) NM may not cause skin sensitization by the same molecular and cellular key events as small organic molecules do; in fact, T-cell-mediated hypersensitivity may not be the most relevant reaction of the immune system to NM. We conclude that the NAMs adopted by OECD test guidelines are currently not a good fit for testing inorganic NM. Full article

Natural language processing (NLP) technology has recently used to predict substance properties based on their Simplified Molecular-Input Line-Entry System (SMILES). We aimed to develop a model predicting human skin sensitizers by integrating text features derived from SMILES with in vitro test outcomes. The dataset on SMILES, physicochemical properties, in vitro tests (DPRA, KeratinoSens^TM, h-CLAT, and SENS-IS assays), and human potency categories for 122 substances sourced from the Cosmetics Europe database. The ChemBERTa model was employed to analyze the SMILES of substances. The last hidden layer embedding of ChemBERTa was tested with other features. Given the modest dataset size, we trained five XGBoost models using subsets of the training data, and subsequently employed bagging to create the final model. Notably, the features computed from SMILES played a pivotal role in the model for distinguishing sensitizers and non-sensitizers. The final model demonstrated a classification accuracy of 80% and an AUC-ROC of 0.82, effectively discriminating sensitizers from non-sensitizers. Furthermore, the model exhibited an accuracy of 82% and an AUC-ROC of 0.82 in classifying strong and weak sensitizers. In summary, we demonstrated that the integration of NLP of SMILES with in vitro test results can enhance the prediction of health hazard associated with chemicals. Full article

Urban regeneration can be defined as a multi-functional, specifical zoning application for the improvement and sustainability of an urban area with its physical, environmental, social and economic conditions. The question of where the urban regeneration will take place constitutes the primary pillar of the applications. Considering the expected high-intensity earthquake in Istanbul, there is a significant number of risky regions in the earthquake zone that need to be regenerated. The important part of reducing damage in an earthquake disaster is improving the quality of the building stock. The identification, prioritization, analysis and visualization of disaster priority regeneration areas (DPRAs) is possible by creating a functional model based on a spatial basis. The main element in the scope of this study is to establish the processes related to the DPRAs and to determine the necessary criteria for the determination of these areas. Analyzing how much the existing DPRAs overlap with the areas suggested in this study and creating basis for the needed model in order to identify the undeclared areas, the destruction and losses that may be caused by the earthquake in the coming years can be prevented by the implementation of this sustainable and integrated urban regeneration model. Full article

Delayed-type hypersensitivity (DTH) is caused by a broad number of drugs used in clinic, and antineoplastic drugs show an elevated proportion of DTH, which potentially affects the quality of life of patients. Despite the serious problem and the negative economic impact deriving from market withdrawal of such drugs and high hospitalization costs, nowadays, there are no standard validated methods in vitro or in vivo to evaluate the sensitizing potential of drugs in the preclinical phase. Enhanced predictions in preclinical safety evaluations are really important, and for that reason, the aim of our work is to adapt in vitro DPRA, ARE-Nrf2 luciferase KeratinoSens^TM, and hCLAT assays for the study of the sensitizing potential of antineoplastic agents grouped by mechanism of action. Our results reveal that the above tests are in vitro techniques able to predict the sensitizing potential of the tested antineoplastics. Moreover, this is the first time that the inhibition of the VEGFR1 pathway has been identified as a potential trigger of DTH. Full article

The Electrophilic Allergen Screening Assay (EASA) has emerged as a promising in chemico method to detect the first key event in the adverse outcome pathway (AOP) for skin sensitization. This assay functions by assessing the depletion of one of two probe molecules (4-nitrobenzenethiol (NBT) and pyridoxylamine (PDA)) in the presence of a test compound (TC). The initial development of EASA utilized a cuvette format resulting in multiple measurement challenges such as low throughput and the inability to include adequate control measurements. In this study, we describe the redesign of EASA into a 96-well plate format that incorporates in-process control measurements to quantify key sources of variability each time the assay is run. The data from the analysis of 67 TCs using the 96-well format had 77% concordance with animal data from the local lymph node assay (LLNA), a result consistent with that for the direct peptide reactivity assay (DPRA), an OECD test guideline (442C) protein binding assay. Overall, the measurement science approach described here provides steps during assay development that can be taken to increase confidence of in chemico assays by attempting to fully characterize the sources of variability and potential biases and incorporate in-process control measurements into the assay. Full article

After the Fukushima Daiichi Accident, the safety features such as accident tolerant fuel (ATF) and diverse and flexible coping strategies (FLEX) for existing nuclear fleets are being investigated by the US Department of Energy under the Light Water Reactor Sustainability Program. This research is being conducted to quantify the risk-benefit of these safety features. Dynamic probabilistic risk assessment (DPRA)-based response-surface approach has been presented to quantify the FLEX and ATF benefits by estimating the risk associated with each option. ATFs with multilayered silicon carbide (SiC), iron-chromium-aluminum, and chromium-coated zirconium cladding were considered in this study. While these ATF candidates perform better than the current zirconium cladding (Zr), they may introduce additional failure modes in some operating conditions. The fuel failure analysis modules (FAMs) were developed to investigate ATF performance. The dynamic risk assessments were performed using RAVEN, a DPRA tool, coupled with RELAP5 and FAMs. A cumulative distribution function-based index provided a mean of comparing the benefits of safety enhancements. For medium break loss of coolant accidents, FLEX operational timing window for each fuel type was estimated. Among these ATF candidates, SiC-type ATF was the most beneficial candidate for an increased safety margin than Zr-based fuel and was found to complement FLEX strategies in terms of risk and coping time. Full article

The dependability assessment is a crucial activity for determining the availability, safety and maintainability of a system and establishing the best mitigation measures to prevent serious flaws and process interruptions. One of the most promising methodologies for the analysis of complex systems is Dynamic Reliability (also known as DPRA) with models that define explicitly the interactions between components and variables. Among the mathematical techniques of DPRA, Stochastic Hybrid Automaton (SHA) has been used to model systems characterized by continuous and discrete variables. Recently, a DPRA-oriented SHA modelling formalism, known as Stochastic Hybrid Fault Tree Automaton (SHyFTA), has been formalized together with a software library (SHyFTOO) that simplifies the resolution of complex models. At the state of the art, SHyFTOO allows analyzing the dependability of multistate repairable systems characterized by a reactive maintenance policy. Exploiting the flexibility of SHyFTA, this paper aims to extend the tools’ functionalities to other well-known maintenance policies. To achieve this goal, the main features of the preventive, risk-based and condition-based maintenance policies will be analyzed and used to design a software model to integrate into the SHyFTOO. Finally, a case study to test and compare the results of the different maintenance policies will be illustrated. Full article

The biological process of skin sensitization depends on the ability of a sensitizer to modify endogenous proteins. A direct peptide reactivity assay (DPRA), based on the biological process of skin sensitization, was developed as an alternative to controversial animal experiments. Although DPRA has been endorsed by industries and is internationally accepted as promising, it has several drawbacks, such as incompatibility with hydrophobic chemicals, inability to perform detailed reaction analysis, and ability to evaluate only single components. Here, we demonstrated that sensitizers and peptide adducts can be easily identified using a mass spectrometry-based solid-phase peptide reaction assay (M-SPRA). We synthesized peptides with a photo-cleavable linker immobilized on resins. We showed the potential of M-SPRA in predicting skin sensitization by measuring the peptide adducts that were selectively eluted from the resin after cleaving the linker post-reaction. M-SPRA provides more detailed information regarding chemical reactivity and accurate assessment of test samples, including mixtures. M-SPRA may be helpful for understanding the binding mechanism of sensitizers (toxicology), which may assist in further refining reactivity assays and aiding in the interpretation of reactivity data. Full article

DPRA (direct peptide reactivity assay) and ADRA (amino acid derivative reactivity assay), which are based on the biological events of skin sensitization, were developed as alternatives to the controversial animal experiments. These assays are described in the OECD (Organization for Economic Co-operation and Development) guideline, Test No. 442C. Although these assays have been endorsed by the industries and internationally accepted as promising and effective tests for in vitro skin sensitization, they suffer from several drawbacks, such as incompatibility with hydrophobic chemicals and complicated sample processing. Here, we demonstrated a chromophore-based solid phase peptide reaction assay in vitro using peptides immobilized on magnetic beads (C-SPRA-MB). We successfully synthesized lysine (Lys) and cysteine (Cys) immobilized on magnetic microbeads. However, Cys immobilized magnetic microbeads showed gradual decomposition of the magnetic beads due to SH oxidation. Using Lys immobilized magnetic microbeads, we demonstrated the capacity of C-SPRA-MB to predict skin sensitization by measuring free amino groups of the Lys after reaction with test chemicals. First, the free amines on the microbeads were reacted with bromophenol blue (BB). Then, by treatment with a saturated solution of Lys, the bound BBs were released and quantified. C-SPRA-MB provides high-throughput and accurate assays for assessments of chemicals, including with low-potency as skin sensitizers and poor water solubility. C-SPRA-MB may be useful for effective prediction of their skin sensitization potential in the process of compound screening, especially in the case of misclassified by DPRA and ADRA. Thus, C-SPRA-MB can be applied to assessing the sensitization potential of medical, pharmaceutical, cosmetics, and industrial compounds. Full article

Irritant and allergic contact dermatitis are undesired side effects in the development of drugs and cosmetics as well as after contact with environmental or industrial chemicals. Over the last decades, a great deal of progress has been made in the development of alternative In vitro test to assess these issues. Driven by the 7th Amendment to the European Cosmetic Directive, the EU policy on chemicals (the registration, evaluation, authorization and restriction of chemicals (REACH) system), the update of the European legislation on the protection of animals used in research, and emerging visions and strategies for predicting toxicity, in vitro methods are likely to play a major role in the near future. On 12 December 2013, the European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM, part of the European Commission Joint Research Centre) published its Recommendation on the Direct Peptide Reactivity Assay (DPRA) for skin sensitization, capable of distinguishing sensitizers from non-sensitizers. Other assays (i.e., KeratinoSens™ assay) will follow shortly. While a number of methods are at various stages of development and use, currently it is not possible to rank chemicals for their sensitizing potency, an issue that is important for a full safety assessment. It is expected that a predictive method to totally replace animal testing will be in the form of a test battery comprising molecular, cell-based, and/or computational methods, the so-called “Integrated Approaches to Testing and Assessment”. This review aims to discuss the state-of-the-art in the field of in vitro assessment of contact sensitizers. Full article