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OMICS Platform

 

Together with the bioinformatics platform, the mission of the OMICS platform is to support the programme in the projects aiming to systematically identify and characterize key regulators in zebrafish, rodents and cells in vitro, as well as in biofilms. To this end, the platform offers services in genomics and transcriptomics via its Next Generation Sequencing (NGS) facility to the programme, as well as external users. During the 2014-2015 period, the NGS facility has been engaged in 42 projects from the programme, as well as 11 projects from external users. Furthermore, the OMICS platform complements this NGS portfolio by including metabolomics and proteomics based on a combination of NMR spectroscopy and mass spectrometry (MS). However, investment is still needed to complement the infrastructure in these areas. Here we outline our most recent developments.

 

Various new protocols for NMR and MS analytics of specific classes of metabolites have been established. For instance, methods for metabolome analysis in the zebrafish have been developed using 1D and 2D 1H NMR techniques. These developments were driven by a project from the Dickmeis lab investigating the zebrafish metabolome in a model of adrenal insufficiency. Subsequently, this method has been applied to analyse the circadian metabolome in larval zebrafish in order to investigate the contribution of metabolic processes to the circadian clock system (Li et al. 2015). On-going projects include for the determination of metabolome changes during cancer development in zebrafish models, and the profiling of mouse muscle metabolism. Our developments in the area of LC-MS-MS have been driven by projects investigating bacterial signalling molecules and secondary metabolites involved in a wide variety of regulation processes, such as biofilm formation, motility and induction of virulence factors (Strehmel et al. 2015; Bouffartigues et al. 2015). Regarding OMICS in biotechnology, several MS and NMR protocols for product characterization were established for the structural characterization of diverse glycolipid based biosurfactants (Kügler et al. 2014, Pöhnlein et al. 2015; Kügler et al. 2015). Moreover, novel fast 2D methods for increased resolution in NMR spectroscopy have been developed for analysing small molecules at natural abundance (Schulze-Sünninghausen et al. 2014).