Skin Sensitisation (Q)SARs/Expert Systems: from Past, Present to Future

This review describes the state of the art of available (Q)SARs/expert systems for skin sensitisation and evaluates their utility for potential regulatory use. There is a strong mechanistic understanding with respect to skin sensitisation which has facilitated the development of different models. Most existing models fall into one of two main categories either they are local in nature, usually specific to a chemical class or reaction chemical mechanism or else they are global in form, derived empirically using statistical methods. Some of the published global QSARs available have been recently characterised and evaluated elsewhere in accordance with the OECD principles. An overview of expert systems capable of predicting skin sensitisation is also provided. Recently, a new perspective regarding the development of mechanistic skin sensitisation QSARs so-called Quantitative Mechanistic Modelling (QMM) has been proposed, where reactivity and hydrophobicity, are used as the key parameters in mathematically modelling skin sensitisation. Whilst hydrophobicity can be conveniently modelled using log P, the octanol-water partition coefficient; reactivity is less readily determined from chemical structure. Initiatives are in progress to generate reactivity data for reactions relevant to skin sensitisation but more resources are required to realise a comprehensive set of reactivity data. This is a fundamental and necessary requirement for the future assessment of skin sensitisation.JRC.I.3-Toxicology and chemical substance

Development of an In Silico Profiler for Respiratory Sensitisation

In this article, we outline work that led the QSAR and Molecular Modelling Group at Liverpool John Moores University to be jointly awarded the 2013 Lush Science Prize. Our research focuses around the development of in silico profilers for category formation within the Adverse Outcome Pathway paradigm. The development of a well-defined chemical category allows toxicity to be predicted via read-across. This is the central approach used by the OECD QSAR Toolbox. The specific work for which we were awarded the Lush Prize was for the development of such an in silico profiler for respiratory sensitisation. The profiler was developed by an analysis of the mechanistic chemistry associated with covalent bond formation in the lung. The data analysed were collated from clinical reports of occupational asthma in humans. The impact of the development of in silico profilers on the Three Rs is also discussed

Peptide reactivity assays for skin sensitisation–scope and limitations

The direct peptide reactivity assay (DPRA) is an OECD test guideline method that aims to determine if a chemical is reactive enough to be a skin sensitiser. It involves incubation of the test chemical at 5 mMolar concentration for 24 h with a cysteine-based peptide at 0.5 mMolar concentration and measurement of the percentage depletion (DP) of the peptide. The kinetic direct peptide reactivity assay (kDPRA) is derived from the DPRA and involves incubating the peptide with the test chemical at a range of concentrations and incubation times to produce a data matrix of DP values, which is analysed to give a reactivity parameter logk max that assigns chemicals to the 1A potency class (high potency) if logk max reaches the threshold value of −2. Here the DPRA, with a threshold of 47% DP, is compared against the kDPRA for their abilities to distinguish between the 1A and non-1A potency classes. It is found that they perform very similarly against a dataset of 157 chemicals with known potency, with only marginal differences in predictive performance. The thresholds of −2.0 (kDPRA) and 47% DP (DPRA) to distinguish 1A sensitisers are not scientific absolutes but the best compromises for a heterogenous set of data containing classes of chemicals for which different thresholds would be applicable. It is concluded that although the kDPRA represents a major advance towards predicting skin sensitisation potency on a continuous basis without animal testing, it offers no significant advantage over the DPRA for the purpose of 1A classification

A critical review of the kinetic direct peptide reactivity assay (kDPRA) for skin sensitizer potency assessment - taking it forward

It is widely recognized that the ability of chemicals to sensitize, and the potency of those chemicals that are sensitizers, is related to their ability to covalently modify protein in the skin. With the object of putting non-animal-based prediction of skin sensitization on a more quantitative footing, a recent paper describes the development of the kinetic Direct Protein Reactivity Assay (kDPRA), in which a matrix of peptide depletion values for different reaction times and test chemical concentrations is generated and analyzed so as to derive a reactivity parameter, logk max, which is used to classify chemicals into one of two potency categories. The present paper demonstrates that the reaction chemistry is not always consistent with the mathematical analysis of the data matrix and the kDPRA protocol does not identify such cases. Consequently the derived logk max value is not always mechanistically meaningful and its application to predict potency can lead to misleading conclusions. It is shown that by adopting a data analysis protocol based on conventional kinetics practice, the kDPRA can be made to provide more reliably meaningful and more extensive information that can be used for purposes such as potency estimation for deriving No Expected Sensitization Induction Level (NESILs) required for quantitative risk assessment (QRA), deriving quality specifications in terms of acceptable impurity levels, and development of structure-activity relationships. Secondly, the paper addresses applicability domain issues, in particular the problem of deciding whether or not the kDPRA is applicable for a given chemical

Interpretation of murine local lymph node assay (LLNA) data for skin sensitization: Overload effects, danger signals and chemistry-based read-across

There is a large body of information on testing of chemicals for skin sensitization in the murine local lymph node assay (LLNA), in which potency is quantified by the EC3 value, derived from dose-response data. This information finds use in risk assessment and regulatory classification, and also in assessing the performance of non-animal methods. However, some LLNA results are not straightforward to interpret, and in some cases published EC3 values are questionable. These cases usually arise where the dose–response does not show a monotonic increasing pattern but is bell-shaped, or shows a decrease in response with increasing dose over the whole dose range tested. By analogy with a long-recognised phenomenon in guinea pig sensitization, this is referred to as the overload effect. Here a mechanistic rationale is presented to explain the overload effect, and at the same time to explain the production of danger signals even when the sensitizer is non-irritant. Some illustrative examples are presented where the overload effect can lead to misinterpretation of LLNA results, and chemistry-based read-across is applied to reinterpret the data

The Effect of Focal Damage to the Right Medial Posterior Cerebellum on Word and Sentence Comprehension and Production

Functional imaging studies of neurologically intact adults have demonstrated that the right posterior cerebellum is activated during verb generation, semantic processing, sentence processing, and verbal fluency. Studies of patients with cerebellar damage converge to show that the cerebellum supports sentence processing and verbal fluency. However, to date there are no patient studies that investigated the specific importance of the right posterior cerebellum in language processing, because: (i) case studies presented patients with lesions affecting the anterior cerebellum (with or without damage to the posterior cerebellum), and (ii) group studies combined patients with lesions to different cerebellar regions, without specifically reporting the effects of right posterior cerebellar damage. Here we investigated whether damage to the right posterior cerebellum is critical for sentence processing and verbal fluency in four patients with focal stroke damage to different parts of the right posterior cerebellum (all involving Crus II, and lobules VII and VIII). We examined detailed lesion location by going beyond common anatomical definitions of cerebellar anatomy (i.e., according to lobules or vascular territory), and employed a recently proposed functional parcellation of the cerebellum. All four patients experienced language difficulties that persisted for at least a month after stroke but three performed in the normal range within a year. In contrast, one patient with more damage to lobule IX than the other patients had profound long-lasting impairments in the comprehension and repetition of sentences, and the production of spoken sentences during picture description. Spoken and written word comprehension and visual recognition memory were also impaired, however, verbal fluency was within the normal range, together with object naming, visual perception and verbal shortterm memory. This is the first study to show that focal damage to the right posterior cerebellum leads to language difficulties after stroke; and that processing impairments persisted in the case with most damage to lobule IX. We discuss these results in relation to current theories of cerebellar contribution to language processing. Overall, our study highlights the need for longitudinal studies of language function in patients with focal damage to different cerebellar regions, with functional imaging to understand the mechanisms that support recovery

Discourse or dialogue? Habermas, the Bakhtin Circle, and the question of concrete utterances

This is the author's accepted manuscript. The final publication is available at Springer via the link below.This article argues that the Bakhtin Circle presents a more realistic theory of concrete dialogue than the theory of discourse elaborated by Habermas. The Bakhtin Circle places speech within the “concrete whole utterance” and by this phrase they mean that the study of everyday language should be analyzed through the mediations of historical social systems such as capitalism. These mediations are also characterized by a determinate set of contradictions—the capital-labor contradiction in capitalism, for example—that are reproduced in unique ways in more concrete forms of life (the state, education, religion, culture, and so on). Utterances always dialectically refract these processes and as such are internal concrete moments, or concrete social forms, of them. Moreover, new and unrepeatable dialogic events arise in these concrete social forms in order to overcome and understand the constant dialectical flux of social life. But this theory of dialogue is different from that expounded by Habermas, who tends to explore speech acts by reproducing a dualism between repeatable and universal “abstract” discursive processes (commonly known as the ideal speech situation) and empirical uses of discourse. These critical points against Habermas are developed by focusing on six main areas: sentences and utterances; the lifeworld and background language; active versus passive understandings of language; validity claims; obligation and relevance in language; and dialectical universalism

Specificity of the local lymph node assay (LLNA) for skin sensitisation

The local lymph node assay (LLNA) has provided a large dataset against which performance of non-animal approaches for prediction of skin sensitisation potential and potency can be assessed. However, a recent comparison of LLNA results with human data has argued that LLNA specificity is low, with many human non-sensitisers, particularly hydrophobic chemicals, being false positives. It has been suggested that such putative false positives result from hydrophobic chemicals causing cytotoxicity, which induces irritancy, in turn driving non-specific lymphocyte proliferation. This paper finds that the apparent reduced specificity of the LLNA largely reflects differences in definitions of the boundaries between weak skin sensitisers and non-sensitisers. A small number of LLNA false positives may be due to lymphocyte proliferation without skin sensitisation, but most alleged ‘false’ positives are in fact very weak sensitisers predictable from structure-activity considerations. The evidence does not support the hypothesis for hydrophobicity-induced false positives. Moreover, the mechanistic basis is untenable. Sound LLNA data, appropriately interpreted, remain a good measure of sensitisation potency, applicable across a wide hydrophilicity-hydrophobicity range. The standard data interpretation protocol enables detection of very low levels of sensitisation, irrespective of regulatory significance, but there is scope to interpret the data to give focus on regulatory significance

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

© 2015 Becraft, Wood, Rusch, Kühl, Jensen, Bryant, Roberts, Cohan and Ward. Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time

Right cerebral motor areas that support accurate speech production following damage to cerebellar speech areas

Specific regions of the cerebellum are activated when neurologically intact adults speak, and cerebellar damage can impair speech production early after stroke, but how the brain supports accurate speech production years after cerebellar damage remains unknown. We investigated this in patients with cerebellar lesions affecting regions that are normally recruited during speech production. Functional MRI activation in these patients, measured during various single word production tasks, was compared to that of neurologically intact controls, and patient controls with lesions that spared the cerebellar speech production regions. Our analyses revealed that, during a range of speech production tasks, patients with damage to cerebellar speech production regions had greater activation in the right dorsal premotor cortex (r-PMd) and right supplementary motor area (r-SMA) compared to neurologically intact controls. The loci of increased activation in cerebral motor speech areas motivate future studies to delineate the functional contributions of different parts of the speech production network, and test whether non-invasive stimulation to r-PMd and r-SMA facilitates speech recovery after cerebellar stroke