Attila Cristian Ratiu

Drosophotoxicology: An Emerging Research Area for Assessing Nanoparticles Interaction with Living Organisms

The rapid development of nanotechnology allowed the fabrication of a wide range of different nanomaterials, raising many questions about their safety and potential risks for the human health and environment. Most of the current nanotoxicology research is not standardized, hampering any comparison or reproducibility of the obtained results. Drosophotoxicology encompasses the plethora of methodological approaches addressing the use of Drosophila melanogaster as a choice organism in toxicology studies. Drosophila melanogaster model offers several important advantages, such as a relatively simple genome structure, short lifespan, low maintenance cost, readiness of experimental manipulation comparative to vertebrate models from both ethical and technical points of view, relevant gene homology with higher organisms, and ease of obtaining mutant phenotypes. The molecular pathways, as well as multiple behavioral and developmental parameters, can be evaluated using this model in lower, medium or high throughput type assays, allowing a systematic classification of the toxicity levels of different nanomaterials. The purpose of this paper is to review the current research on the applications of Drosophila melanogaster model for the in vivo assessment of nanoparticles toxicity and to reveal the huge potential of this model system to provide results that could enable a proper selection of different nanostructures for a certain biomedical application.

Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions.

BackgroundA critical topic of insertional mutagenesis experiments performed on model organisms is mapping the hits of artificial transposons (ATs) at nucleotide level accuracy. Mapping errors may occur when sequencing artifacts or mutations as single nucleotide polymorphisms (SNPs) and small indels are present very close to the junction between a genomic sequence and a transposon inverted repeat (TIR). Another particular item of insertional mutagenesis is mapping of the transposon self-insertions and, to our best knowledge, there is no publicly available mapping tool designed to analyze such molecular events.ResultsWe developed Genome ARTIST, a pairwise gapped aligner tool which works out both issues by means of an original, robust mapping strategy. Genome ARTIST is not designed to use next-generation sequencing (NGS) data but to analyze ATs insertions obtained in small to medium-scale mutagenesis experiments. Genome ARTIST employs a heuristic approach to find DNA sequence similarities and harnesses a multi-step implementation of a Smith-Waterman adapted algorithm to compute the mapping alignments. The experience is enhanced by easily customizable parameters and a user-friendly interface that describes the genomic landscape surrounding the insertion. Genome ARTIST is functional with many genomes of bacteria and eukaryotes available in Ensembl and GenBank repositories. Our tool specifically harnesses the sequence annotation data provided by FlyBase for Drosophila melanogaster (the fruit fly), which enables mapping of insertions relative to various genomic features such as natural transposons. Genome ARTIST was tested against other alignment tools using relevant query sequences derived from the D. melanogaster and Mus musculus (mouse) genomes. Real and simulated query sequences were also comparatively inquired, revealing that Genome ARTIST is a very robust solution for mapping transposon insertions.ConclusionsGenome ARTIST is a stand-alone user-friendly application, designed for high-accuracy mapping of transposon insertions and self-insertions. The tool is also useful for routine aligning assessments like detection of SNPs or checking the specificity of primers and probes. Genome ARTIST is an open source software and is available for download at www.genomeartist.ro and at GitHub (https://github.com/genomeartist/genomeartist ).

Relative quantification of Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia and Aggregatibacter actinomycetemcomitans high-risk bacterial species in Romanian patients evaluated for periodontal disease

Three bacterial species pertaining to the red complex (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) and Aggregatibacter actinomycetemcomitans were investigated in relation to the incidence and severity of periodontal disease. A total of 259 patients were included in this study, 179 being diagnosed with periodontal disease. The gingival crevicular fluid samples were obtained from periodontal pockets and the presence and levels of target bacteria were assessed following DNA extraction and real-time quantitative PCR. Our results account for significant positive associations between the number of bacterial species from the red complex coexisting within a patient and several clinical signs (gingival bleeding, inflammation and bone deterioration). A similar positive association was found between bacterial load of the red complex species and the clinical Case Type diagnostic of the periodontal disease, as well as the probing depth with the most evident results for T. denticola. In conclusion, our study, a first for the Romanian population, confirms previous results found elsewhere and finds a possible regional pathogenic specificity for T. denticola as a major factor for periodontitis severity.Three bacterial species pertaining to the red complex (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) and Aggregatibacter actinomycetemcomitans were investigated in relation to the incidence and severity of periodontal disease. A total of 259 patients were included in this study, 179 being diagnosed with periodontal disease. The gingival crevicular fluid samples were obtained from periodontal pockets and the presence and levels of target bacteria were assessed following DNA extraction and real-time quantitative PCR. Our results account significant positive associations between the number of bacterial species from the red complex coexisting within a patient and several clinical signs (gingival bleeding, inflammation and bone deterioration), the Case Types of the periodontal disease and probing depth. In conclusion, this study on the subject of critical periodontal pathogens quantification it is a first revealing a glimpse of the bacterial dynamics and its effects on periodontal disease severity in the Romanian population.

Insertion patterns of P{lacW} and P{EP} artificial transposons on the third chromosome of Drosophila melanogaster

Insertional mutagenesis experiments performed on Drosophila melanogaster model often relies on induced mobilization of artificial transposons derived from P mobile element. In an attempt to detect transposition preferences, we accomplished a pilot study concerning the insertional patterns of P{lacW} and P{EP} constructs in the third chromosome of D. melanogaster. Our inventory inquiry considered 2177 insertions of P{lacW} and 1646 insertions of P{EP} available in FB2016_02 release of FlyBase and revealed insertional hotspots and coldspots in 3L and 3R, but also a preference of both artificial transposons to insert in 3R. The general distribution of P{lacW} and P{EP} insertions appears to be similar but not identical, probably due to differences in size and molecular architecture of these transposons. Our results may have predictive value for experimental design of insertional mutagenesis screenings, but are also expected to contribute to a better understanding of P transposon biology.