Content

The integrated practical is divided in several themes, each consisting of a series of experiments revolving around a central research question. These themes cover a wide range of wet lab as well as dry lab techniques, integrating the fields of molecular biology, immunology, genetic manipulation of organisms, data analysis and bioinformatics. In addition to the lab practical sessions, there is also a part that focusses on academic writing. The students will maintain/acquire awareness of plagiarism and GenAI by using the Toledo tutorial "Information literacy KU Leuven libraries (Science and Technology)" (NL/EN) and testing it. The test is not compulsory.

Experimental evolution of a Pseudomonas fluorescens strain to study newly emerging morphotypes

• Evolution experiment using different growth conditions
• Assessment of competitive fitness of ancestor strain versus evolved mutant
• Sequence analysis to find underlying mutations of variant morphotype
   

Causality testing of a single point mutation for increased persistence in Escherichia coli

• Amplification and purification of mutant allele DNA
• Creation of mutant bacterium carrying mutant allele
• Phenotypic testing of newly obtained mutant for increased persistence
• Statistical analysis of results from persistence assay
   

Studying resistance development of Pseudomonas aeruginosa over the past half-century

• Processing raw sequencing data and performing de novo genome assembly
• Genome annotation and database search for antibiotic-resistance conferring mutations
   

Heterologous expression and detection of phage proteins in E. coli

• Recombinant expression and fractionation of phage proteins
• Visualization of different protein fractions and specific detection and quantification of recombinant proteins
• In silico protein purification
   

Identification of protein-protein interactions in Saccharomyces cerevisiae

• Transformation of bait and prey protein-encoding plasmids in mutant S. cerevisiae strain
• Phenotypic screen for interaction between recombinant proteins
• Phenotypic screen for interaction between recombinant proteins

Gene discovery by virus-induced gene silencing in tobacco

• Design of construct for RNAi mediated gene silencing
• Transformation of construct in Agrobacterium and infection of Nicotiana benthamiana
• Phenotypic testing for gene silencing symptoms and comparing expression levels of silenced plants with control plants
   

Performing in silico proteomics analysis using open-source software

• Processing and analysis of mass spectrometry data from proteins interacting with a bait protein
• Identification and functional analysis of interactor proteins

Academic writing exercise

• Elaborating on scientific literature related to experiments performed in the lab

If, for reasons of force majeure, the faculty decides that the laboratory sessions cannot go ahead in their current form, compulsory attendance will be waived. The changes resulting from the force majeure situation will be announced on Toledo as soon as they are known.

Course material

Manual, planning and extra information is available on Toledo.