Ateneo - UPO

Synthetic biology is an emerging field that spans the boundary of biology, engineering, and physical sciences with its goal of engineering biomolecular systems and cellular capabilities for a variety of applications. This course aims to offer an introduction to this rapidly evolving field and equip students with foundational skills and critical mindsets that are required for synthetic biology research. Advanced molecular biology tools for DNA assembly, the construction of biological pathways and circuits, genome editing, and strategies for transcriptional control will be examined in the course.

Fu P, Panke S. Systems Biology and Synthetic Biology (2009). John Wiley & Sons, Inc., Hoboken, New Jersey ISBN: 978-0-470-43797-1

Liljeruhm J, Gullberg E, Forster AC. (2014). Synthetic Biology – a lab manual. World Scientific Publishing Co, Singapore

Smolke C, Lee SY, Nielsen J, Stephanopoulos G. Synthetic Biology: Parts, Devices and Applications. Wiley-Blackwell. ISBN: 978-3-527-33075-1

Zhao H. Synthetic Biology: Tools and Applications. Academic Press.
ISBN 978-0-12-394430-6. DOI https://doi.org/10.1016/C2011-0-06857-6

The course aims to provide students with an overview of the recently developed molecular tools that are used for the in vivo monitoring of cellular events and/or perturbation of biological systems. In particular, the course will provide an in-depth overview of the state-of-the-art methodologies and techniques used for the design and fabrication of biological components and systems that do not already exist in the natural world, and the re-design of existing biological systems.

Good knowledge of molecular and cellular biology of Eukaryotes and Prokaryotes

Teaching methods include lectures, active learning in the classroom and
at distance. Classroom activities:
- Lectures supported by presentations (PowerPoint) with graphic
illustrations, mind maps,
animation films of cellular processes
- Classroom activities with active student participation (representation of
cellular processes, instant polls, termination of exercises).
Activities and online material (moodle):
- educational material presented in class.
- Video recordings replacing the lectures
- Quiz, forums and workshops for learning and self-assessment

Support activity (tutoring/students with disabilities/working students)
• Students can ask questions and find study support through the moodle
teaching forum.
• Examples of exam tests are provided in online activities on moodle.
• Students with disorders that can affect learning (for example, colorblind, visually impaired, hearing-impaired, dyslexic or physically disabled students) are invited to contact the lecturer in order to adapt the
teaching material, face-to-face and online activities and their method
of verification.

Evaluation of Learning/Grades
Discussion, Quizzes, Homework – 20%
Written Proposal – 50%
Final Exam – 30%

Discussion, Quizzes, Homework.
Throughout the semester there will be quizzes, discussions, and homework assigned for grades that will represent 20% of the final grade.

Proposals
Each student will be responsible for writing a research proposal that aims to investigate a novel idea in the field of synthetic biology that is of scientific or industrial interest. The proposal should be structured according to a template provided by the teacher. Each student will also be assigned two proposals prepared by other classmates and will draw up a written report that critically review the proposals. The written proposal + critical review will represent 50% of the final grade.

Final Exam
There will be a final exam administered at the ordinary sessions (February, June-July, and September). All material covered during class will be subject to testing. Tests are conceptually cumulative because understanding of topics covered early in the course will be required to understand materials covered later in the course. The final exam will represent 30% of the final grade.

Introduction to Synthetic Biology (SynBio): The “Biology 4.0” revolution.
Milestones of Recombinant DNA technology: bacteria, plasmids, phages, restriction endonucleases, DNA polymerases, DNA ligases, Polymerase chain reaction (PCR), DNA sequencing.
Biological Parts: genes, promoters, regulators, terminators, open reading frames.
Bioinformatic tools. Oligonucleotide design, restriction analyses, codon optimization, virtual cloning.
Cloning techniques and strategies. The “scar-less” DNA Cloning: Gibson assembly, Golden gate cloning, Ligation-independent cloning (LIC).
SynBio strategies: the “bottom-up” and the “top-down” approaches. The “design-build-test-learn” cycle.
From cell-free systems to the artificial cell.
Cloning DNA without a template: the chemical synthesis and assembly of DNA.
Cell reprogramming by synthetic DNA: JCVI syn1-3.0 and the “recoded” E. coli. The “minimal genome project” and the “Genome Project-Write”.
Genome Engineering Technologies: Transposons, Recombinases, Zinc Fingers, TALEN’s, CRISPR/Cas9
Synthetic circuits and Metabolic Engineering.
Applications of SynBio in the field of Medical Biotechnologies:
Biosensors: genetically engineered gut bacteria to detect cancer in vivo
Gene and cell therapies: CAR-T cells
Cell factories to produce recombinant proteins
Pharmaceuticals: semi-synthetic artemisinin, cannabinoids.
Sustainable Foods: Golden rice, lab-grown meat
Genetically engineered probiotics
Biomaterials and tissue engineering
Diagnostics, therapeutics, and vaccines: lessons from SARS-CoV-2
Ethical issues: Biosafety and biocontainment, Dual Use Research of Concern (DURC), “Do-it-yourself” (DIY) Biology
Patentability and entrepreneurship of SynBio.

NOTE: The course programme, which provides 6 credits, is identical in content to the "Synthetic Biology" module of the course "Synthetic Biology and Proteomics" (curriculum B - Systems Biomedicine), which provides 5 credits. The 6 hours of difference between the two courses will be used to organize Journal clubs in which students, divided into groups, will present scientific articles on topics related to Synthetic Biology.

Students enrolled in this course will be able to:
1. Define synthetic biology and understand its importance in the 21st century
2. Understand and describe biological parts and their function on the systems level.
3. Understand advanced molecular biology techniques that facilitate the building of biological parts and systems.
4. Apply a scientific approach to the planning, execution, reporting and interpretation of advanced projects with the aim at creating replicating systems with new properties that can be regulated, and to critically analyze the results and generate testable hypotheses from these experiments
5. critically analyze, present, and defend scientific literature in synthetic biology, including practical applications such as cell and metabolic engineering
6. Consider ethical decisions and containment strategies in synthetic biology