Molecular Biology Techniques

Objectives

The Molecular Biology Techniques subject is taught in a project-based learning (PBL) format.

The experimental project consists in the identification of an organism through the DNA barcoding technique, which is based on the amplification and sequencing of a mitochondrial gene fragment: Cytochrom oxidase I (CO1).

Throughout the project, several molecular biology techniques are introduced, discussed and applied, while reinforcing different technical and cross-curricular skills.

Subject aims

• Observe at all times the safety and operation regulations in the laboratory.
• Manipulate properly the routine-use laboratory instruments and correctly apply microbiology and molecular biology protocols.
• Record in a proper and orderly manner all the activities carried out in the laboratory.
• Understand and successfully apply protocols for extraction, amplification and analysis of nucleic acids.
• Carry out the molecular identification of a species of insect from a tissue sample.

Sustainable Developement Goals

This subject addresses the study of global and local biodiversity in the context of the following SDGs:

• Goal 14. Life Below Water - Conserve and sustainably use the oceans, seas and marine resources
• Goal 15. Life On Land - Biodiversity, Forests, Desertification

Learning outcomes

• LO1. Gains autonomy and initiative in the laboratory.
• LO2. Properly uses routine-use instruments in a biological laboratory, including safety and disposal regulations.
• LO3. Plans the execution and carries out an experimental protocol in a team-work context and in a suitable time.
• LO4. Keeps an adequate activity record and issues reports that justify and analyze the work done.
• LO5. Performs a critical interpretation of the experimental results to draw reasonable conclusions.
• LO6. Understands the basics of basic molecular biology techniques and applies them correctly.
• LO7. Searches the necessary bibliographical resources.
• LO8. Understands and is able to communicate complex oral and written messages.
• LO9. Writes written reports and documents with proper spelling and grammar.

Competencies

Specific skills

• Have oral and written skills in English for communicating results, conclusions and processes deriving from research in the field of biology.
• Manipulate databases used in the field of biology. 
• Master basic laboratory techniques in biology, apply protocols and use appropriate instruments, observing safety norms and correctly interpreting the results obtained.
• Understand the processes of functional integration in organisms based on knowledge of subcellular structure and organism cell types. 

Basic skills

• Students can apply their knowledge to their work or vocation in a professional manner and have competencies typically demonstrated through drafting and defending arguments and solving problems in their field of study.
• Students have demonstrated knowledge and understanding in a field of study that builds on general secondary education with the support of advanced textbooks and knowledge of the latest advances in this field of study.

Core skills

• Be a critical thinker before knowledge in all its dimensions. Show intellectual, cultural and scientific curiosity and a commitment to professional rigour and quality.
• Use oral, written and audiovisual forms of communication, in one's own language and in foreign languages, with a high standard of use, form and content.

Content

1. Introduction to laboratory work
   1. Basic laboratory regulations
   2. Reagent manipulation and waste disposal
   3. Team work organisation
2. Introduction to the Barcode of Life Project: Molecular-based identification of species
   1. Sample collection
   2. Gathering and organisation of sample metadata
3. Amplification and sequencing of cytochrome oxidase I (CO1)
   1. PCR amplification
   2. Sanger sequencing
4. Data analysis
   1. Data pre-processing and quality check
   2. Sequence alignment and identification
   3. Introduction to the phylogenetic analysis of sequences

Evaluation

Assessment activities (which represent 100% of the final mark (F.M.))

• Activity 1: Written test (40% of the F.M.). Minimum grade: 4/10. Resit allowed
• Activity 2: Team work public exposition (15% of the F.M.). Resit not allowed
• Activity 3: Exercises and final report (30% of F.M.). Resit not allowed (late submission penalises 20%)
• Activity 4: Personal performance and attitude in the laboratory (15% of the F.M.). Resit not allowed

Additional considerations

• Attendance at all sessions is mandatory. Justified absence up to a maximum of 20% of sessions.
• Unjustified absence to more than 20% of the sessions (or justified absence to more than 40%) results in a grade of 0/10 of activity 4.
• Absence to more than 40% of the practical activities implies failing the subject.
• The lack of punctuality will be assessed negatively and, if it is repeated and unjustified, it will be considered absence.
• Activity 2: Unjustified absence to final exposition results in a grade of 0/10 and a penalisation of 25% on the grade obtained by the group to which the student belongs.
• Activity 4 will assess the following aspects:
  • Proper work in the laboratory and correct use and care of basic materials and techniques.
  • Understanding and correct application of the laboratory protocols.
  • Results obtained in the practical experiments.

Methodology

• The methodology of the project is based on the development of an eminently hands-on laboratory activity.
• Various resources and activities, both guided and self-study, are contemplated, which must allow students the adequate achievement of the competences, skills and knowledge associated with the protocols that will be developed throughout the sessions.

Bibliography

Bibliography

• W. John Kress and David L. Erickson, Editors (2012). DNA Barcodes: Methods and Protocols. Springer.

Reading

Teachers will provide complementary bibliography and compulsory reading throughout the course via the Virtual Campus.