Summer Schools in Applied Molecular Microbiology

John Innes/Rudjer Bošković
Summer Schools in Applied Molecular Microbiology

Inter-University Centre (IUC) in Dubrovnik
Dubrovnik
Piece of architecture

Content and format of the 2012 course

Topics to be covered:

  • isolation and screening of metabolite-producing microorganisms;
  • natural products in microbial communities and cell-cell interactions;
  • natural products in symbioses with higher organisms;
  • genomic enzymology of antibiotic resistance;
  • regulation of metabolism and intracellular signalling;
  • metagenomics and heterologous pathway expression;
  • genome sequencing, annotation and comparative genomics;
  • genomics-driven methods for novel natural product discovery;
  • characterisation of biosynthetic pathways in silico and experimentally;
  • pathway engineering and combinatorial biosynthesis.

Hands-on computer workshops will be a unique aspect of the course. These will go well beyond the topics covered in previous summer schools. Microbial genomes can now be sequenced in a matter of days. Automated annotation is fast becoming the preferred method of annotation as opposed to the careful manual annotation of just a few years ago. Transcriptomics is moving from microarray hybridization to RNA-seq and protein DNA interactions are being studied at the whole-genome level by ChIP-seq. The first workshop and associated lecture will describe the formats of data coming from such high-throughput technologies and demonstrate tools and methods for turning these data into conclusions and knowledge. The second workshop will introduce software and web sites for the identification and analysis of metabolic gene clusters, especially, but not exclusively, those for polyketides and non-ribosomal peptides. These websites are ideal for analysing cryptic biosynthetic gene clusters and making structural predictions about their metabolic products, providing examples of the increasing power of bioinformatics for deducing details of biosynthetic pathways from DNA sequences and hence aiding in the discovery of novel, useful compounds. The associated lecture, after the workshop, will describe examples of the experimental discovery of novel metabolites using the principles developed in the workshop.

A typical working day will include lectures in the morning, computer workshops and small group discussions in the afternoon, and guest talks and poster sessions in the evening; all participants will be asked to bring a poster. There will be free time on the working days and one day will be devoted to an all-day excursion. There will be a welcome mixer party on the day of arrival and a farewell party on the final evening before departure the next day.

The course will be limited to 40-45 participants.

Venue

The 2012 Summer School will be held at the Inter-University Centre (IUC) in Dubrovnik. The Centre has bedroom accommodation on the top floor and fine facilities for lectures and seminars, computer teaching, poster viewing and spaces for small group discussions and relaxation. Swimming from a rocky bathing spot is a few minutes' walk from the Centre and the Old City of Dubrovnik is also very close. A sandy beach is less than 30 minutes' walk away. Transfers from the airport are easy: the airport bus to town stops very close to the IUC.