Ateneo - UPO

The course provides a rigorous theoretical and practical foundation in Synthetic Biology, tracing its development from the milestones of recombinant DNA technology to the most advanced genome engineering and synthetic genomics approaches. It covers standardized biological parts, bioinformatic design tools (oligonucleotide design, codon optimization, virtual cloning), “scar-less” cloning strategies (Gibson assembly, Golden Gate, LIC), the “design–build–test–learn” cycle, genome engineering technologies (ZFNs, TALENs, CRISPR/Cas9) and synthetic circuits/metabolic engineering. A major part of the course addresses biomedical applications of Synthetic Biology: biosensors, gene and cell therapies (CAR-T cells), cell factories for recombinant protein production, semi-synthetic pharmaceuticals, sustainable foods, engineered probiotics, biomaterials and diagnostics/vaccines, drawing on lessons from the SARS-CoV-2 pandemic. The extended edition (36 hours) additionally covers the ethical, regulatory and entrepreneurial dimensions: biosafety and biocontainment, Dual Use Research of Concern (DURC), the “Do-It-Yourself” (DIY) Biology movement, and the patentability and entrepreneurship of SynBio innovations.

●      Christina Smolke (Editor), Sang Yup Lee (Series Editor), Jens Nielsen (Series Editor), Gregory Stephanopoulos (Series Editor), Synthetic Biology: Parts, Devices and Applications. Wiley-VCH (2018), ISBN: 978-3-527-33075-1●      Paul Simon Freemont, Richard I. Kitney, Synthetic Biology - A Primer, Imperial College Press,●      Natalie Kuldell, BioBuilder, O'Reilly Media, ISBN 1491904291●      Huimin Zhao (Ed), Synthetic Biology. Tools and Applications. Academic press. Hardback ISBN: 9780123944306, eBook ISBN: 9780123978202●  Liljeruhm J, Gullberg E, Forster AC. Synthetic Biology – a lab manual. World Scientific Publishing Co, Singapore

The course aims to provide MSc students in Medical Biotechnologies with an advanced, interdisciplinary preparation in Synthetic Biology, integrating the foundations of classical genetic engineering with the most recent technologies for designing, building and programming biological systems. The goal is to train professionals able to understand, critically evaluate and contribute to the development of innovative biomedical applications — gene and cell therapies, biosensors, drugs and vaccines, biomaterials — while respecting principles of biosafety, ethics and sustainability, and with full awareness of the regulatory, patenting and entrepreneurial dimensions of the field.

● Molecular biology and genetics (gene expression, transcription, translation, recombinant DNA technology)
● Cell biology (prokaryotic and eukaryotic cell structure and function)
● Basic biochemistry (enzymes, metabolic pathways, protein structure)
● Fundamentals of biotechnology (GMOs, cloning strategies, PCR)
● Elementary quantitative skills (basic mathematics and statistics)

● Lectures. Frontal lectures with slides and live demonstrations of bioinformatics/design tools (virtual cloning, codon optimization).
● Journal Club. Critical reading and guided discussion of selected high-impact primary research papers.
● Design Exercises. In-class design exercises (oligonucleotide design, restriction analysis, virtual cloning, circuit design).
● Student Presentations. Brief group presentations on cutting-edge topics or recent publications.
● Extended Module Seminars. Seminar-style sessions (Units 16–18) on biosafety, DIY Biology and patentability/entrepreneurship, with instructor facilitation.

Students with disabilities, Specific Learning Disorders (SLD), or Special Educational Needs (SEN) may request specific services and tools dedicated to them by contacting the Staff for Career Development and Coordination and Services for Students, and by consulting the dedicated page on the University's website. After getting in touch with the University Staff, they may contact the instructor responsible for the course to agree on exam procedures and teaching-related aspects.
Attendance: attendance at in-person lectures is mandatory for all degree programs (minimum 50%-66% of hours, corresponding to at least 15 hours - curriculum B; 24 hours - curriculum C; 12 hours - curriculum D). Students who do not reach the minimum threshold will not be admitted to the exam in the current session.
Working students and individuals in particular situations (caregivers, etc.) are invited to contact the instructor within the first week of classes to agree on alternative arrangements, in compliance with the University Regulations.
Accessible materials: slide PDFs are provided in text format (not scanned); recorded distance-learning (DAD) lectures are accompanied by subtitles or transcripts.

Learning Assessment / GradesDiscussion, quizzes, and homework (continuous assessment) — 34%Written project proposal — 33%Project discussion at the exam — 33%Discussion, quizzes, and homework During the semester, quizzes, discussions, and homework will be assigned that will contribute to the student's continuous assessment. This component accounts for 34% of the final grade.Project Each student will be responsible for drafting a research project aimed at investigating a new 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 instructor. The evaluation of the written proposal accounts for 33% of the final grade.Final exam A final exam is scheduled, during which each student will discuss their own project, to be taken during one of the regular exam sessions (February, June-July, September). The discussion will cover the project's content and the related course material; the topics are conceptually cumulative, as understanding the material covered earlier in the course is necessary to grasp the topics covered later. This component accounts for 33% of the final grade.

The course consists of 18 didactical units of 2 hours each (36 hours total). Units 1–15 (30 hours) are shared with the curricula B and C; Units 16–18 (6 hours) are exclusive to the curriculum C.
UD_1: Introduction to Synthetic Biology The "Biology 4.0" revolution: from reading to writing and editing life. Historical trajectory of Synthetic Biology (SynBio) as a discipline; relationship with classical genetic engineering; overview of the course, its main applications, and the ethical frameworks that will be explored.
UD_2: Key milestones in recombinant DNA technology Fundamental tools of molecular biology: bacteria as host organisms, plasmids, phages; discovery and use of restriction enzymes; DNA polymerases and DNA ligases; the polymerase chain reaction (PCR); the evolution of DNA sequencing technologies.
UD_3: Biological parts The building blocks of synthetic constructs: genes, promoters, regulators, terminators, open reading frames (ORFs); principles of part standardization and characterization.
UD_4: Bioinformatics tools for SynBio design Oligonucleotide design; restriction site analysis; codon optimization; virtual/in-silico cloning; overview of software and online platforms supporting the design-build cycle.
UD_5: Cloning techniques and strategies Classical and modern cloning strategies; "scar-less" DNA cloning methods: Gibson assembly, Golden Gate cloning, Ligation-Independent Cloning (LIC).
UD_6: SynBio strategies and the design cycle "Bottom-up" and "top-down" approaches to Synthetic Biology; the "Design-Build-Test-Learn" (DBTL) cycle; from cell-free systems to the artificial cell.
UD_7: Template-free DNA cloning Chemical synthesis of oligonucleotides and genes; DNA assembly strategies for template-free construction of genes, pathways, and genomes.
UD_8: Cellular reprogramming through synthetic DNA Whole-genome synthesis and cellular reprogramming: JCVI-syn1.0, syn2.0, and syn3.0; "recoded" E. coli; the Minimal Genome Project; the Genome Project-Write (GP-write) initiative.
UD_9: Genome engineering technologies Tools for targeted genome modification: transposons, recombinases, zinc finger nucleases (ZFN), TALENs, and the CRISPR/Cas9 system.
UD_10: Synthetic circuits and metabolic engineering Principles of synthetic gene circuit design; logic and feedback control; metabolic engineering strategies for the biosynthesis of target molecules.
UD_11: Applications in Medical Biotechnology I: Biosensors and cell therapies Biosensors: genetically engineered gut bacteria for in vivo cancer detection; gene and cell therapies: CAR-T cells as a Synthetic Biology product.
UD_12: Applications in Medical Biotechnology II: Cell factories and drugs Engineered cell factories for recombinant protein production; pharmaceutical applications: artemisinin and semi-synthetic cannabinoids.
UD_13: Applications in Medical Biotechnology III: Sustainable food and probiotics Sustainable foods obtained through SynBio: Golden Rice, lab-grown meat; genetically modified probiotics for therapeutic and nutritional purposes.
UD_14: Applications in Medical Biotechnology IV: Biomaterials and diagnostics Biomaterials and tissue engineering; diagnostics, therapies, and vaccines: lessons learned from the SARS-CoV-2 pandemic.
UD_15: Ethical issues in Synthetic Biology Biosafety and biocontainment strategies; Dual Use Research of Concern (DURC) and its governance; the "Do-It-Yourself" (DIY) Biology movement and its social implications.
UD_16: Biosafety, biocontainment, and dual-use research (Extended module) In-depth analysis of biocontainment strategies for engineered organisms; regulatory and governance frameworks for Dual Use Research of Concern (DURC); international biosafety guidelines.
UD_17: The "Do-It-Yourself" (DIY) Biology movement (Extended module) Origins and philosophy of the DIY Bio/biohacking movement; community labs and citizen science; opportunities and risks of democratized biotechnology; case studies and current debates.
UD_18: Patentability and entrepreneurship in Synthetic Biology (Extended module) Intellectual property and patentability of synthetic biology parts, devices, and organisms; open-source biology vs. proprietary innovation; entrepreneurship, start-ups, and technology transfer in the SynBio sector.

Shared outcomes (Units 1–15)●      Describe the historical milestones of recombinant DNA technology and situate Synthetic Biology within the “Biology 4.0” revolution.●      Identify and characterize standardized biological parts (genes, promoters, regulators, terminators, ORFs) used in synthetic constructs.●      Use bioinformatic tools for oligonucleotide design, restriction analysis, codon optimization and virtual cloning.●      Apply “scar-less” cloning strategies (Gibson assembly, Golden Gate cloning, LIC) and evaluate bottom-up and top-down SynBio strategies within the design–build–test–learn cycle.●      Explain template-free DNA synthesis and assembly, and describe whole-genome synthesis projects (JCVI-syn1.0–3.0, recoded E. coli, minimal genome project, GP-write).●      Compare genome engineering technologies, including transposons, recombinases, ZFNs, TALENs and CRISPR/Cas9.●      Design and analyse synthetic circuits and metabolic engineering strategies for the biosynthesis of biomedically relevant molecules.●      Evaluate biomedical applications of Synthetic Biology, including biosensors, gene and cell therapies, cell factories, pharmaceuticals, sustainable foods, engineered probiotics, biomaterials and SARS-CoV-2-related diagnostics/vaccines.Additional outcomes (Units 16–18, curr C only)●      Assess biosafety, biocontainment strategies and the governance of Dual Use Research of Concern (DURC).●      Critically discuss the “Do-It-Yourself” (DIY) Biology movement and its societal and regulatory implications.●      Analyse the patentability of synthetic biology inventions and the entrepreneurial pathways for translating SynBio research into products and start-ups.