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Tara Oceans scienceResearch Teams

Rainer Pepperkok

Rainer Pepperkok
E-mail
ALMF
EMBL Heidelberg, Germany

The Advanced Light Microscopy Facility (ALMF) offers a collection of state-of-the-art light microscopy equipment and image processing tools. The facility was set up as a cooperation between EMBL and industry to improve communication between users and producers of high-end microscopy technology and to support in-house scientists and visitors in using light microscopy methods for their research. The ALMF also organises regular international courses to teach advanced light microscopy methods.

  • The ALMF presently manages 19 top-of-the-line microscope systems plus nine High-Content Screening microscopes from leading industrial companies, as well as five image analysis workstations.
  • More than 30 visitors per year come to carry out their own experiments in the ALMF or to evaluate microscopy equipment.
  • The ALMF was the seed for the European Light Microscopy Initiative (ELMI) that establishes links with facilities throughout Europe.
  • Usage of the facility has exceeded 30,000 hours per year. In the context of TARA OCEANS, Rainer Pepperkok will apply the use of high content light microscopy techniques to the quantitative analysis of microplankton organisms and further develop this tool to allow the establishment of correlation between species identification at the genomics and and morphologic level in collaboration with other members of TARA OCEANS.

Relevant publications

  1. Ritzerfeld, J., Remmele, S., Wang, T., Temmerman, K., Brugger, B., Wegehingel, S., Tournaviti, S., Strating, J.R., Wieland, F.T., Neumann, B., Ellenberg, J., Lawerenz, C., Hesser, J., Erfle, H., Pepperkok, R. & Nickel, W. Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of Src kinases. Genome Res. 2011 Jul 27.
  2. Conrad, C., Wunsche, A., Tan, 2. T.H., Bulkescher, J., Sieckmann, F., Verissimo, F., Edelstein, A., Walter, T., Liebel, U., Pepperkok, R. & Ellenberg, J. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods. 2011 Jan 23.
  3. Neumann, B., Walter, T., Heriche, J.K., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wünsche, A., Satagopam, V., Schmitz, M.H., Chapuis, C., Gerlich, D.W., Schneider, R., Eils, R., Huber, W., Peters, J.M., Hyman, A.A., Durbin, R., Pepperkok, R. & Ellenberg, J. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 2010 Apr 1;464(7289):721-7.
  4. Gilbert, D.F., Meinhof, T., Pepperkok, R. & Runz, H. DetecTiff(C): A Novel Image Analysis Routine for High-Content Screening Microscopy. J Biomol Screen. 2009 Jul 29.
  5. Starkuviene, V., Pepperkok, R. & Erfle, H. Transfected cell microarrays: an efficient tool for high-throughput functional analysis. Expert Rev Proteomics. 2007 Aug;4(4):479-89.

Recruitment
1 postdoc to develop high-throughput automated imaging and quantification of small protists in the 5-50 µm size range.
For application, please send your CV to Rainer.