GCC 2017 has ended
The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

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Thursday, June 29 • 15:40 - 17:00
P31: In silico toxicity assessment in cultured rat intestinal cells deduced from cellular impedance measurements and transcriptomics data

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Pooja Gupta 1,2,*, Soroush Sharbati 3, Ralf Einspanier 3, Christof Schuette 1,2, Annika Gramatke 3, Max von Kleist 1, Jutta Sharbati 3

1 : Institute of Mathematics, Freie Universität Berlin
2 : Mathematics for Life and Materials Sciences, Zuse Institute Berlin
3 : Institute of Veterinary Biochemistry, Freie Universität Berlin
* : Corrsponding author

Predicting adverse effects of chemicals with respect to their distinguishing temporal and dose-dependent mode of action denotes a formidable challenge in toxicological research. In this project, we addressed the aforementioned problems by developing a framework for predicting the toxicity of chemicals using real-time cell impedance measurements and transcriptomics data (mRNA and miRNA) obtained from rat intestinal cell line IEC-6.

Real-time cell impedance measurements provide a novel, fast and cost effective in vitro method that may be used to probe compounds' toxicity. In order to improve the interpretability and usability of this experimental method, we developed a mathematical model for quantifying the cytotoxicity of chemicals (in terms of its 50% inhibitory concentration IC50 and cell growth rate). Estimated IC50 values for the apparently toxic compounds were in good agreement with literature knowledge. Furthermore, a computational analysis of the transcriptomics data was undertaken to identify the ‘molecular mechanism of action' of the test chemicals. Our analysis showed that 2-acetylamino-fluorene and benzo-[a]-pyrene were severely genotoxic, with several genes differentially expressed even at very low doses.

Taken together, by developing a foundation work for modeling impedance measurements and analyzing transcriptomics datasets for predicting cytotoxicity, our study contributed to the goal of improving in vitro strategies for genotoxicity testing.

avatar for Pooja Gupta

Pooja Gupta

Bioinformatician, Universitätsklinikum Erlangen

Thursday June 29, 2017 15:40 - 17:00 CEST
Le Corum Le Corum

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