Molecular Microbiology

Molecular Microbiology is a discipline that combines genetics, physiology, biochemistry, molecular biology and cytology with microbiology. These fields have undergone dramatic, in some cases almost explosive, developments during the last decade. In particular, genetic engineering of microorganisms has become very efficient with rapid methods of gene mutation and replacement and rapid whole genome sequencing; biochemistry has been revolutionized by methods for rapid protein purification and crystallization and high-throughput protein-protein interaction detection methods whereas cytology has been revolutionized by the introduction of fluorescent protein tags and a number of high-end methods to visualize the fluorescently tagged proteins within living cells. Last but not least, the genomics era has spawned a genuine revolution in microbiology, transforming it into an exact discipline. There are now more than 8,000 fully sequenced and annotated prokaryotic genomes available. Making use of this vast biological information is now possible to classify prokaryotes numerically and thereby choose model systems of general importance.

The present course in Molecular Microbiology is taught by researchers belonging to the Sections of Functional Genomics and of Biomolecular Science. It is our aim with the course to give a broad overview of both the fundamental knowledge and the rapidly developing and exciting topics in Molecular Microbiology. Emphasis is placed on the molecular mechanisms underlying bacterial stress physiology, which is essential for bacterial survival in the environment, and thereby tolerance and resistance to antibiotics. The topics will be discussed in lectures given by researchers and also in theoretical excises(i.e. colloquium) where in-depth discussion of recent research articles will be presented by the students with guidance from the instructors. Finally, in the laboratory exercise part, relevant critical and cutting-edge techniques will be used to investigate research problems that we currently study in the laboratory. This comprehensive course will thus provide a strong platform for those students who wish to pursue or already are pursuing a research career in molecular microbiology and also in areas connected with general microbiology.

The theoretical part (lectures and colloquia) will contain an in-depth discussion of molecular topics such as:

• Techniques used to study molecular microbiology
• Basic bacterial physiological processes, such as DNA replication, gene transcription, protein translation
• How bacteria under stress reprogram their physiology by using e.g. intracellular second messengers ppGpp
• How bacteria under stress reprogram their transcription patterns using alternative RNA polymerase sigma factors
• How bacteriophages interactwith and hijack bacterial cells 
• Molecular mechanisms of bacterial translation and its dynamic regulation in response to stresses
• Bacterial ribonucleases and small regulatory RNA molecules
• Molecular mechanisms underlying bacterial survival during stationary phase

• The connection between growth rate, ribosome synthesis and translation
   

The practical part (lab exercises):

The practical part of the course will consist of a full-time two-week lab course. During that time the students will be introduced to several techniques within the field of molecular microbiology, including:

• Basic methods for propagation of bacteria in the laboratory
• Purification of DNA (plasmid, genome) from bacterial cells 
• Using reporter genes to analyze gene expression
• PCR and genetic construction of site-directed mutant genes and proteins
• Molecular cloning techniques
• DNA sequencing and sequence analysis
• Study of protein-protein interactions by using a two-hybrid system
• Analyzing protein structure using Pymol
• Strategies for proper documentation of laboratory experiments and results
• Discussion of the obtained results