TP5

Project TP5: Technology-plattform

Responsible: Michael Hecker, Thomas Schweder and Jörg Bernhardt, IMaB

 

Development of databases and software for the integration, evaluation and visualization of project data {Jörg Bernhardt and Michael Hecker (IMaB) in cooperation with Frank Oliver Glöckner and Hanno Teeling (Jacobs)

The multitude of heterogeneous data that will be generated during this project, calls for the development of new databases and adequate software tools for state-of-the-art genome-based analyses of marine ecosystems. This will be accomplished by an extension of the existing Marine2D database (developed at the IMaB; www.marine2d.de) and of the sequence annotation and analysis pipeline (developed in Bremen). Cross-linking these systems with the Genomes Mapserver (www.megx.net/mm) that was established during the ongoing EU project MetaFunctions, would allow for the collection and evaluation of additional environmental parameters from satellite data. New analysis- and visualization methods will be designed to evaluate and illustrate the genome- and expression data in conjunction with diversity and sampling site-specific physicochemical parameters. 

 

Mass spectrometry (Michael Hecker)

This part of the project will provide the technological basis for both gel-based and gel-free high-throughput analyses of protein extracts from marine samples. This platform will meet the particular requirements of marine metaproteomics by using the highly sensitive peptide fractionation method. One of the main issues in this project is the establishment of 1D gel-based and gel-free protein identification methods. This sub-project is supposed to cover the expected high demand of analysis capacity. New methods for the separation of highly complex protein mixtures are to be developed. Existing methods for the isolation, identification and quantification of proteins are to be adapted to the requirements of marine metaproteome analyses. Furthermore, new high-throughput de novo peptide sequencing procedures will be established. 

 

Sequencing (Thomas Schweder in coordination with Rudolf Amann (MPI), Frank Oliver Glöckner (Jacobs) und Klaus Jürgens (IOW))

The comprehensive collection of sequence data from environmental samples is one of the technical basics of this joint project. Major resources are designated for the sequencing of the metagenome libraries from the sub-projects 3 and 4. The thus obtained sequence data are essential for the entire project. Especially, pyrosequencing will be used for gene expression analysis of pure model cultures (for methodical optimization), as well as on the sampling sites Helgoland and Gotland Deep. The required DNA samples will be taken as parallels to the respective samplings in sub-project 3. The combination of gene expression analyses and simultaneous collection of sequence data is expected to give information about active metabolic genes of the most abundant populations of microorganisms at the sampling site.