TECNOLOGIES FOR THE ENVIRONMENT

Module MOLECULAR PHYLOGENESIS LABORATORY

Knowledge and understanding

By the end of the course, students will have acquired basic and advanced theoretical knowledge of the evolutionary relationships between organisms and the mechanisms of phylogeny at a molecular level. They will understand the fundamental principles of the main laboratory techniques (DNA extraction, PCR, electrophoresis and sequencing), models of molecular evolution and the logical algorithms underpinning phylogenetic reconstruction methods (Neighbour-Joining, Maximum Parsimony, Maximum Likelihood).

Applied knowledge and understanding

Students will be able to apply the skills they have learnt in practice through experimental and bioinformatics work. Specifically, they will be able to extract genomic DNA, set up a PCR amplification reaction and perform agarose gel electrophoresis. They will also be able to independently use the main bioinformatics tools for editing chromatograms, querying databases (GenBank, BLAST) and multiple sequence alignment (CLUSTAL, MAFFT) in order to generate and visualise phylogenetic trees.

Independence of judgement

The student will develop the ability to critically assess the accuracy of molecular data and the effectiveness of different phylogenetic reconstruction methods in relation to the various taxonomic levels analysed. They will be able to independently interpret the results generated by bioinformatics software and select the markers.

Communication skills

Students will be able to express the theoretical concepts and methodological procedures learnt during lectures and laboratory sessions clearly, fluently and using rigorous scientific language. They will be able to accurately describe the logic behind an experimental design, the interpretation of a chromatogram and the structure of a phylogenetic tree, demonstrating their linguistic skills both in the oral examination and during teamwork in the laboratory.

Learning skills

The course will provide students with the methodological and IT tools necessary to continuously update their knowledge in the fields of molecular biology and bioinformatics. Students will develop an independent study methodology that will enable them to critically review the scientific literature, access public databases and independently undertake further advanced study or work in biomedical and environmental professional contexts.

Attendance is compulsory, as stipulated in the degree programme’s academic regulations.

Participation in laboratory activities is essential for acquiring the required practical skills.

The final examination consists of an oral examination on the topics covered during the lectures.

Assessment is based on a mark out of 30, with a minimum pass mark of 18/30, which is averaged with the mark from the examination for the other module. 

Assessment criteria:

- knowledge and understanding of the subject matter;

- ability to apply and interpret the material;

- ability to integrate knowledge across disciplines;

- accuracy and appropriateness of scientific language;

- relevance of the answers;

- clarity of presentation.

What are the main methods of phylogenetic reconstruction?

What is the principle behind PCR amplification, and how do you prepare a reaction mix?

What can the BLAST tool be used for?