a Whole Genome Array Approach - Jacobs University

Research Aims
2.3 Design of the whole genome array of Rhodopirellula baltica
In 1999, Lander called DNA microarrays 'arrays of hope' because for the first time it was
possible to take “global views” of biological processes at the genome level (Lander 1999).
This statement nicely matches the expectations linked to the whole genome array of the
marine planctomycete Rhodopirellula baltica. The design of the array was driven by the
ambition to understand more about the role of R. baltica, representing the phylum
Planctomycetes as one of the key players in the carbon cycle and about its adaptation
mechanisms to changing environmental conditions and cell biology. Microarray-mediated
expression profiling should also to help reveal regulation-patterns of the large number of
genes encoding hypothetical proteins.
A conventional whole genome array targeting all 7325 genes annotated within the R. baltica
genome (Glöckner et al. 2003) is set up within the framework of the Network of Excellence
Marine Genomics Europe (MGE). So far, no universal microarray hybridisation protocol was
available (Li et al. 2002). Therefore, every slide type or chemical surface, every new target
preparation process and labelling method, hybridisation and washing buffer composition as
well as hybridisation time and conditions have to be optimised corresponding to the new
application. Moreover, the specific proteinaceous cell wall of R. baltica makes it difficult to
apply common RNA extraction, cDNA-transcription and labelling methods, and thus requires
substantial methodological adaptations.
In parallel, a pipeline for microarray data processing and data storage has to be implemented.
Different microarray data analysis software tools are reviewed with the focus on usability and
calculation transparency. Moreover, a database for storing the data in-house needs to be
initiated. The validation/quality of the resulting data during the optimisation process needs to
be checked by the spotted positive and negative controls and consistency with published
results of proteome studies (Gade et al. 2003; Gade et al. 2005).
20