DNA Manipulation and Synthetic Biology

Code:

BIOL4055

Acronym:

BIOL4055

Level:

400

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2025/2026 - 1S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Master in Applications in Biotechnology and Synthetic Biology

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:ABBS	22	Study plan since academic year 2025/2026	1	-	6	42	162

Teaching language

Suitable for English-speaking students

Objectives

Provide the basic concepts and terminology related to Synthetic Biology, and advanced concepts on DNA manipulation and recombinant DNA technologies using a synthetic biology approach. Familiarization with the design of synthetic modules and circuits and use of bioinformatics tools for codon optimization and in silico construction. Understand how the expression of heterologous proteins can be modulated, using for example different regulatory elements. Familiarization with the analysis of original scientific articles, logic of experimental design  and data analysis. Training in oral and written communication.

 

Learning outcomes and competences

Acquire knowledge on the rationale for the design of synthetic modules and circuits and the underlying molecular processes such as gene expression and regulation. Understanding the experimental requirements for the production of genetically modified organisms and expression of heterologous proteins.
Ability to use bioinformatics tools for sequence analysis, codon optimization, and in silico construction using the Registry of Standard Biological Parts.

Laboratory skills in analysis of recombinant protein expression (SDS-PAGE/Western blot).
Ability to analyze the results obtained using the acquired knowledge and ability to propose strategies to improve the performance of synthetic modules/circuits.

Ability to analyze relevant scientific articles and to integrate the knowledge.

Development of oral communication skills.

Working method

Presencial

Program

Introduction to synthetic biology. Notion of standardized biological part (bio-bricks) and codon optimization. Database and repository of biological parts. Construction of modules and circuits and integration into a chassis. Chassis requirements. Main research areas in Synthetic Biology. Modification of genetic/metabolic pathways for specific applications. BioModularH2, Cyanofactory and PhotoBioCat projects as case studies.

Sequence analysis and codon optimization. In silico construction of a synthetic circuit for the production of hydrogen.


Cultivation of genetically modified cyanobacteria. Protein extraction and quantification. Analysis of protein extracts by SDS-PAGE and SDS-PAGE/Western Blot.

Discussion of the results obtained according to the knowledge acquired.

Presentation and discussion of an article/scientific project by the students.

 

 

Mandatory literature

Videira Arnaldo 340; Engenharia genética. ISBN: 9789727577439

Complementary Bibliography

Watson James D. 1928- 070; Recombinant DNA. ISBN: 9781429203128
Sambrook Joseph; Molecular cloning. ISBN: 978-087969-577-4 (Vol. 1)
Greenfield Edward A., 1957- 340; Antibodies. ISBN: 9781936113811

Teaching methods and learning activities

The use of real examples of research and "case studies", provide the context of reality and allows the acquisition of the notion that science is a continuous search for answers to questions that are never completely solved.

Students are encouraged to ask questions, engage in group activities and to take the initiative to investigate specific topics. Activities include lectures, discussion groups, tutorials, problem solving etc. 

Assessment tools include presentation and discussion of scientific article/project  and a final exam.

keywords

Natural sciences > Biological sciences > Biological engineering > Genetic engineering
Natural sciences > Biological sciences > Biology > Molecular biology

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Exame	80,00
Apresentação/discussão de um trabalho científico	20,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	120,00
Frequência das aulas	42,00
Total:	162,00

Eligibility for exams

Compulsory class attendance (minimum 3/4)

Calculation formula of final grade

Final Exam (16 points) + Oral presentation (4 points)

Classification improvement

Final Exam (16 points)

Observations

Coordination: Paula Tamagnini pmtamagn@fc.up.pt


Júri: Paula Tamagnini, Paulo Oliveira, Catarina Pacheco