International reference centre for the genomics and diagnosis of viruses with small circular DNA

Composition of the EU-funded consortium 2007-2010 (ERA-PG)
 

  • Prof. Dr. H. Jeske, Universität Stuttgart, Biologisches Institut (Coordinator)
  • Prof. Dr. E.R. Bejarano, Universidad de Malaga, Facultad de Ciencias, Dpt. Cellular Biology, Genetics and Physiology
  • Dr. B. Gronenborn, Centre National de la Recherche Scientifique, Institut des Sciences du Végétal
  • Dr. S. Ullmann, Qiagen GmbH, Nucleic Acid Preparation Research
     

What are the aims?


The objective of the proposed project is to develop Rolling Circle Amplification (RCA)-based techniques for a worldwide market serving as a low cost alternative to PCR, immunology and cloning. To achieve this goal, the general applicability to various virus species has to be established. Samples from all over the world will be tested for a reliable detection of geminiviruses and nanoviruses.

To facilitate the exchange of material, the simplest way of sample preparation has to be developed. Preferably, this will be a solid support adsorption procedure using special matrices, which retain nucleic acids or nucleic acid-protein complexes, can be dried everywhere and upon rehydration release their cargo in well-equipped laboratories. Such a two-step procedure will overcome the technical limitations in many laboratories of tropical and subtropical countries.

The RCA protocol will be optimized for a broad range of virus-species. RCA products will be used for diagnosis either using various restriction enzymes to detect Restriction Fragment Length Polymorphisms (RFLPs) or for direct sequencing. Whereas RCA/RFLP will be developed for low-budget diagnostic entities, RCA-sequencing will be applicable for a large range of molecular biological laboratories in well-equipped institutions.

RCA has a high capacity for scaling down the reaction volume. Procedures will be developed to miniaturize the reaction in a "lab-on-a-chip" approach. Micro-arrays will be produced to identify circular DNA viruses on the genus, species and strain level. Sequencing of RCA samples will be optimized and automated to establish high-throughput analysis for geminiviruses and nanoviruses. These efforts shall result in an international reference centre. Representative DNA samples are to be collected, catalogued, and RFLP patterns entered into a database which is meant for open access for all interested scientists.

Further international collaborations
 

The EU-funded consortium invites colleagues from all over the world to participate in the reference center initiative.

What do we offer?

During the EU project and up to the capacities of our three laboratories we are able to analyse samples from infected plants using RCA/RFLP. Our aim is to analyse as many different plant species (including crops and weeds) and DNA viruses as possible to validate the suitability of this approach. To this end, scientific colleagues as well as plant protection agencies may send their samples to one of our laboratories and the analysis will be done without any charge. If new virus species will be detected during RCA/RFLP diagnosis, their DNA sequences will be determined and infectious clones will be generated.

 

Final reports of the two SummerSchools that were held at the Universität Stuttgart during this project