91159 - Systems and Synthetic Microbiology

Learning outcomes

By the end of the course, the student has knowledge on the integrative approaches and strategies to study a microorganism as a complex system and to discover and model its properties in the context of synthetic biology, gene regulation, and microbial genome engineering across multiple scales. In particular, the course provides the student with systems and synthetic biology understanding of microorganisms and microbial ecosystems with industrial and environmental interest for biotechnological applications.

Course contents

The course introduces the principles of Systems Biology and Synthetic Biology applied to microorganisms and microbial communities, with particular emphasis on environmental, industrial, and biotechnological applications.

1. Introduction to Systems Biology

• Systems biology as an integrated approach to the study of complex biological systems.
• Integration of omics disciplines for the analysis of cellular functions.
• Microorganisms as complex biological systems.

2. Fundamentals of Synthetic Biology

• Principles of synthetic biology.
• Synthetic biology as a tool for the design and construction of biological systems.
• Relationships between systems biology and synthetic biology.

3. Genetic Engineering and Genome Editing

• Genetic engineering strategies for synthetic microbiology.
• Genome editing technologies.
• Genetic manipulation of microorganisms of biotechnological interest.

4. Biological Networks and Systems Approaches

• Concept of biological networks.
• Representation of biological networks as graphs.
• Analysis of network properties and organization.

5. Synthetic Biological Parts and Genetic Circuits

• Design and characterization of synthetic biological parts.
• Genetic circuits in microbial systems.
• Synthetic biology tools for genetic and metabolic engineering (e.g. BioBrick, pSEVA).

6. Metabolic Engineering and Synthetic Pathways

• Principles of metabolic engineering.
• Design and construction of synthetic metabolic pathways.
• Expression and optimization of artificial pathways in microorganisms.

7. Synthetic and Minimal Genomes

• Concepts and strategies for the construction of synthetic genomes.
• Minimal genomes and their applications.
• Future perspectives in synthetic biology.

8. Systems Biology Applied to Microbial Biotechnology

• Principles of metabolic networks.
• Systems-level approaches in microbial biotechnology.
• Analysis and discussion of case studies from the scientific literature.

Throughout the course, recent scientific papers and applied case studies will be discussed. Students will be actively involved in the critical analysis of scientific literature related to the topics covered.

Readings/Bibliography

Required Material for Exam Preparation

• Lecture slides and teaching materials provided by the instructor.
• Scientific articles and review papers assigned during the course and made available online.

Recommended Reading

• Review papers and scientific publications recommended by the instructor during the course.
• Additional teaching materials made available through the Virtuale platform.

Teaching methods

The course is delivered through:

• lectures supported by multimedia presentations;
• guided discussion of scientific articles;
• analysis of case studies;
• group activities in class;
• student presentations.

Teaching activities are designed to provide students with both theoretical knowledge and critical skills for the analysis of scientific literature and the discussion of topics related to systems and synthetic microbiology.

Students have the right to refuse the registration of a positive grade once, in accordance with the University Teaching Regulations (Art. 16, paragraph 5).

Students with Specific Learning Disorders (SLD) or temporary/permanent disabilities are encouraged to contact the relevant University Office (https://site.unibo.it/studenti-con-disabilita-e-dsa/it ) well in advance. The Office will propose any necessary accommodations, which must be submitted to the instructor for approval at least 15 days before the examination date. The instructor will evaluate the appropriateness of the requested accommodations in relation to the learning objectives of the course.

Students with officially recognized “working student” status should refer to the dedicated University webpage (https://www.unibo.it/it/studiare/guida-alla-scelta-del-corso/conciliare-studio-e-lavoro ) for information on eligibility requirements and available support measures.

 

Assessment methods

The assessment is designed to evaluate:

• knowledge of the principles of systems biology and synthetic biology;
• the ability to understand and discuss genetic and metabolic engineering strategies;
• the ability to critically interpret and discuss scientific literature;
• the ability to use appropriate scientific terminology.

 

Students may choose between the following assessment options.

Option A (available only during the 1st exam session)

Scientific Poster Presentation (20% of the final grade)

Students prepare and present a scientific poster based on a research article or case study related to topics covered during the course.

The presentation evaluates:

• understanding of scientific literature;
• scientific communication and synthesis skills;
• critical analysis of scientific results.

Oral Examination (80% of the final grade)

The oral examination consists of 2–3 questions covering the topics addressed during the course.

The examination evaluates:

• knowledge and understanding of course contents;
• ability to connect different topics within the course;
• appropriate use of scientific terminology.

Option B (available during all the other exam sessions)

Written Examination (100% of the final grade)

The written examination consists of 5–6 open-ended questions covering the theoretical and applied aspects discussed during the course.

Answers should be concise, accurate, and scientifically sound. 

Assessment Criteria

Evaluation will take into account:

• accuracy and completeness of acquired knowledge;
• ability to integrate concepts from different topics covered during the course;
• critical analysis of scientific literature;
• appropriate use of scientific language and terminology;
• clarity of presentation and argumentative skills.

Indicatively:

• 18–21: knowledge of fundamental concepts and basic understanding of the topics covered;
• 22–25: good knowledge of the subject matter and ability to apply acquired concepts;
• 26–29: thorough knowledge, good integration of concepts, and solid critical analysis skills;
• 30–30 cum laude: comprehensive mastery of the subject, excellent analytical and integrative skills, and outstanding scientific communication abilities.

During examinations, the use of textbooks, notes, electronic devices, or any other supporting materials is not permitted unless otherwise specified by the instructor.

The use of AI is prohibited in all assessments. Any use of AI constitutes a breach of academic integrity.

 

Teaching tools

The course makes use of:

• PowerPoint presentations made available through the Virtuale platform;
• selected scientific articles and review papers;
• supplementary teaching materials;
• case studies discussed during lectures;
• open-source videos supporting specific topics when appropriate.

Teaching materials are selected to promote independent learning and ensure accessibility of course content for all students.

Links to further information

https://site.unibo.it/molecular-environmental-microbiology-lab/it/teaching

Office hours

See the website of Martina Cappelletti