The Max Planck Institute for Infection Biology (MPIIB), one out of currently 76 institutes operated by the Max Planck Society for the Advancement of Science, an independent German non-for-profit public body dedicated to perform outstanding basic research, is among Europe's centres of excellence committed to biological research in the field of infectious diseases.  Its Department of Immunology uses multi-disciplinary research approaches to infection biology, comprising concepts and methodologies of molecular genetics, immunology, cell biology, molecular epidemiology and clinical research.  It particularly aims at a better understanding of the biology of mycobacterial pathogens and the identification and structural/functional characterisation of mycobacterial molecules essential for intracellular survival as well as for virulence and persistence.

Facility description

MPIIB's Microarray/Genomics Core Facility (CFM) has got all relevant microarray processing hard- and software necessary for transcriptomic and genomic profiling, including an ozone-free room. QC of RNA preparations, concentration quantification and measurement of dye incorporation is performed by a microfluidics Lab-on-a-Chip system (Agilent Bioanalyzer) and a micro-volume UV-VIS spectrophotometer (Nanodrop ND-1000). Image acquisition from hybridised microarrays is carried out by a high-resolution laser scanning system (Agilent G2565CA). Several image processing programmes (Agilent Feature Extraction, Masqot-GUI) as well as microarray data analysis systems (Rosetta Resolver, GeneSpring, Bioconductor) are available, allowing broad in-depth analyses of the experimental data.

Main staff involved (leaders only)

PI: Prof. Stefan H.E. Kaufmann, Ph.D., Biologist, member of the Max Planck Society, Founding Director of MPIIB, Professor at the Charité Berlin and Dr. h.c. (U Marseille). Over 600 peer reviewed publications and numerous reviews on immunology and infection. Member of the German Academy of Scientists ''Leopoldina'', Berlin Brandenburg Academy of Sciences, and of numerous scientific societies and committees. Numerous awards.

Scientist-in-charge / Dept.: Jeroen Maertzdorf, Biologist, received his Ph.D. from University of Rotterdam in 2002. Staff scientist at Dept. of Immunology since 2007. Main interest: Identification of biomarkers of tuberculosis infection with emphasis on viral co-infection.

Scientist-in-charge / CFM: Hans-Joachim Mollenkopf, Biologist, received his Ph.D. from University of Würzburg in 1995. Since then staff scientist at MPIIB. Since 2002 Head of CFM. 14 years of experience in studying M. tuberculosis, recent 8 years main focus on array-based high-throughput experiments.

Technician-in-charge / Dept. and CFM: Karin Hahnke, Senior Biotechnologist. Since 2001 at Dept. of Immunology. Supervisor of department's transcriptomics experimental work.

Tasks in the the project

MPIIB performs biomarker identification and characterisation, namely global gene expression analyses by using catalogue or custom-tailored Agilent microarrays. MPIIB provides a flexible platform for a network of laboratories involved in clinical vaccine trials with the aim of harmonising global gene expression profiling for monitoring of vaccines in trials.

Transnational Access Services Offered

CFM provides all necessary equipment and software as well as expert knowledge comprising technical advice, experimental help and user specific training in transcriptomic and genomic profiling. Typically, upon request all wetlab work and data analysis will be carried out by CFM following the specific user demands agreed upon beforehand. Experimental steps include RNA extraction, quantification and QC, amplification and labelling of the samples, array hybridisation and washing, image acquisition and feature extraction, data normalization and filtering, and may include statistical analysis and interpretation of experimental results.