In silico model for mutagenicity (Ames test), taking into account metabolism.

Bacterial reverse mutation test is one of the most common methods used to address genotoxicity. The experimental test is designed to include a step to simulate mammalian metabolism. The most common metabolic activation system is the incubation with S9 fraction prepared from the livers of rodents. Usually, in silico models addressing this endpoint are developed on the basis of an overall call disregarding the fact that the toxic effect was observed before or after metabolic activation. Here, we present a new in silico model to predict mutagenicity as measured by activity in the bacterial reverse mutation test, bearing in mind the role of S9 activation to stimulate metabolism. We applied the software SARpy, which identifies structural alerts associated with the effect. Different rules codified by these structural alerts were found in case of positive or negative mutagenicity, observed in the presence or absence of the S9 fraction. These rules can be used to understand the role of metabolism in mutagenicity better. We also identified a possible association of the results from these models with carcinogenicity.

Aquatic toxicity of several textile dye formulations: Acute and chronic assays with Daphnia magna and Raphidocelis subcapitata.

Dyes are widely used in various sectors and can be released into the environment where they persist for a long time because of their high stability to light or temperature and their resistance to environmental degradation. Dyes are often poorly characterized and toxicological/ecotoxicological data are available only for a few. These features, coupled with their toxicity, make dyes a possible source of ecological concern, particularly for freshwater aquatic ecosystems. Therefore, new data may be very useful for their risk assessment. In the present study, we investigated the aquatic toxicity of 42 commercial dye formulations using the application of in silico tools and ecological bioassays. The in silico approach was used to assess the similarities among the dyes, highlighting that dyes from the same chemical class are generally similar. No correlation was found among dyes with the same color. Acute and long-term ecotoxicological assays with daphnids and algae were applied to evaluate the potential impact of these products, according to the OECD guidelines 201 and 202. The bioassays were able to identify structures with potential ecotoxicity: only 9 formulations showed toxicity lower than 100mg/L for daphnids while 30 dyes were toxic for algae. In our experimental conditions, algae were more sensitive to dye toxicity, particularly when the effects on cell number were considered.

Characterization of human gene locus CYYR1: a complex multi-transcript system.

Cysteine/tyrosine-rich 1 (CYYR1) is a gene we previously identified on human chromosome 21 starting from an in-depth bioinformatics analysis of chromosome 21 segment 40/105 (21q21.3), where no coding region had previously been predicted. CYYR1 was initially characterized as a four-exon gene, whose brain-derived cDNA sequencing predicts a 154-amino acid product. In this study we provide, with in silico and in vitro analyses, the first detailed description of the human CYYR1 locus. The analysis of this locus revealed that it is composed of a multi-transcript system, which includes at least seven CYYR1 alternative spliced isoforms and a new CYYR1 antisense gene (named CYYR1-AS1). In particular, we cloned, for the first time, the following isoforms: CYYR1-1,2,3,4b and CYYR1-1,2,3b, which present a different 3' transcribed region, with a consequent different carboxy-terminus of the predicted proteins; CYYR1-1,2,4 lacks exon 3; CYYR1-1,2,2bis,3,4 presents an additional exon between exon 2 and exon 3; CYYR1-1b,2,3,4 presents a different 5' untranslated region when compared to CYYR1. The complexity of the locus is enriched by the presence of an antisense transcript. We have cloned a long transcript overlapping with CYYR1 as an antisense RNA, probably a non-coding RNA. Expression analysis performed in different normal tissues, tumour cell lines as well as in trisomy 21 and euploid fibroblasts has confirmed a quantitative and qualitative variability in the expression pattern of the multi-transcript locus, suggesting a possible role in complex diseases that should be further investigated.