Ateneo - UPO

The module introduces students to the engineering of biological systems, with a deliberate emphasis on the regulatory, biosafety and governance dimension of the discipline. Over 24 hours (12 didactical units), the course examines the core design tools of synthetic biology — standardized parts, cloning and genome-assembly strategies, genome engineering technologies, gene circuits and metabolic engineering — always in relation to the regulatory instruments, biosafety frameworks and governance debates that accompany them (the Asilomar legacy, DURC oversight, EMA/FDA approval pathways for ATMPs, GMO and gene-edited organism regulation, intellectual property law). The final four units are entirely dedicated to biosafety/DURC governance and to intellectual property, the DIY Bio movement and the global regulatory outlook.

●      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●      Regulatory and governance resources: NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules; relevant EMA/FDA guidance documents on Advanced Therapy Medicinal Products (Units 9–10); NSABB reports on Dual Use Research of Concern; EU regulatory materials on genetically modified and gene-edited organisms.●      Supplementary resources: Selected primary research and policy articles distributed via the course page (one per didactical unit); iGEM Registry of Standard Biological Parts (parts.igem.org); Benchling and SBOL Visual for circuit design exercises.

The module aims to provide MSc students in Medical Biotechnologies with the conceptual and technical foundations of synthetic biology, with particular emphasis on the regulatory and governance framework that shapes its development, assessment and deployment. As a component of the integrated course “Preclinical Studies and Regulatory Aspects”, the module prepares students to connect synthetic biology principles to regulatory pathways (FDA/EMA), biosafety and DURC governance systems, intellectual property, and preclinical project planning, in coordination with the other two modules of the integrated course (In vitro and in vivo Preclinical Models; Project Design and Management).

● 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 computational/bioinformatics tools.●      Journal Club. Critical reading and guided discussion of selected primary research and regulatory-guidance articles.●      Design Exercises. In-class design exercises using online platforms (e.g., Benchling, SBOL Visual).●      Regulatory Case Studies. Analysis of real regulatory dossiers and governance case studies (e.g., ATMP approvals, DURC review cases) in Units 9–12.●      Integrative Sessions. Cross-module discussions in Units 9–12, conducted jointly when possible with instructors from the other two modules.

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 module is organized into 12 teaching units of 2 hours each (24 hours total). Units 1–8 are shared with students of the standalone Synthetic Biology courses (30h and 36h). Units 9–12 are exclusive to this integrated course and constitute the regulatory core of the module.UD_1: Introduction to Synthetic Biology and its Regulatory FrameworkThe "Biology 4.0" revolution: from reading to writing and editing life. Historical trajectory of synthetic biology (SynBio); relationship with classical genetic engineering; first overview of international governance bodies (WHO, OECD, Cartagena Protocol) that frame the discipline; course introduction.UD_2: Milestones of Recombinant DNA Technology and Origins of Biosafety RegulationBacteria, plasmids, and phages as tools; restriction endonucleases, DNA polymerase, and ligase; PCR; evolution of DNA sequencing. The Asilomar Conference (1975) and the NIH Guidelines as the founding act of biotechnology regulation.UD_3: Biological Parts, Standardization, and Biosafety ClassificationGenes, promoters, regulators, terminators, and ORFs; principles of part standardization and characterization; risk-group classification of biological parts, organisms, and host-vector systems.UD_4: Bioinformatics Design Tools and the Design–Build–Test–Learn CycleOligonucleotide design, restriction site analysis, codon optimization, and in-silico cloning; the DBTL cycle; "bottom-up" and "top-down" approaches; biosecurity screening of gene synthesis orders.UD_5: Cloning Techniques, Genome Assembly, and Template-Free DNA Synthesis"Scar-less" cloning (Gibson assembly, Golden Gate, LIC); chemical synthesis of oligonucleotides and genes; assembly strategies for template-free construction of genes, pathways, and genomes; oversight of commercial gene synthesis providers (IGSC, Common Mechanism).UD_6: Whole Genome Synthesis, Minimal Genomes, and the GP-write Governance DebateJCVI-syn1.0/syn2.0/syn3.0 and "recoded" E. coli; the Minimal Genome Project; the Genome Project-Write (GP-write) initiative; the related ethical and governance debate on synthetic genomes.UD_7: Genome Engineering Technologies and Regulation of Gene-Edited OrganismsTransposons, recombinases, ZFNs, TALENs, and CRISPR/Cas9; comparative regulatory treatment of gene-edited organisms in the EU, US, and Japan.UD_8: Synthetic Circuits, Metabolic Engineering, and Regulation of Environmental ReleasePrinciples of synthetic genetic circuit design, logic, and feedback control; metabolic engineering for biosynthesis of target molecules; biocontainment requirements and regulatory pathways for environmental and agricultural release of engineered organisms.UD_9: Medical Applications I – Biosensors and Cell/Gene Therapies: Regulatory Pathways for ATMPsEngineered biosensors (e.g., gut bacteria for cancer detection); CAR-T cells as a synthetic biology product; FDA and EMA regulatory pathways for advanced therapy medicinal products (ATMPs); IND/IMPD data packages.UD_10: Medical Applications II – Cell Factories, Engineered Drugs, and Foods: Approval PathwaysCell factories for recombinant proteins; semi-synthetic artemisinin and cannabinoids; Golden Rice, cultured meat, and engineered probiotics; approval frameworks for biotech drugs and novel foods (EFSA, FDA).UD_11: Biosafety, Biocontainment, and Governance of Dual-Use Research of Concern (DURC)In-depth analysis of biocontainment strategies for engineered organisms; DURC governance frameworks; institutional biosafety committees; case studies, including debates on gain-of-function research.UD_12: Intellectual Property, DIY Biology, and the Global Regulatory Future of Synthetic BiologyPatentability of biological parts, devices, and organisms; open-source vs. proprietary innovation; origins and risks of the DIY Bio/biohacking movement; comparative overview of global regulatory frameworks and emerging policy directions.

Core outcomes (Units 1–8, shared)
● Describe the historical and technical milestones that shaped synthetic biology, from recombinant DNA technology to whole-genome synthesis.
● Select, characterize and standardize biological parts, and apply bioinformatic tools within the Design–Build–Test–Learn cycle.
● Apply cloning, genome-assembly and template-free DNA synthesis strategies, and critically discuss their associated biosecurity oversight.
● Explain genome engineering technologies (ZFNs, TALENs, CRISPR/Cas9) and compare how different jurisdictions regulate gene-edited organisms.
● Design and analyse synthetic gene circuits and metabolic engineering strategies, and relate them to biocontainment and environmental-release requirements
Integrative / regulatory outcomes (Units 9–12, module-specific)
● Map the regulatory pathways (FDA, EMA) applicable to synthetic-biology-derived medical products, biosensors, cell and gene therapies, biotech pharmaceuticals and engineered foods, and identify the preclinical data packages they require.
● Critically evaluate biocontainment and biosafety strategies and the governance of Dual Use Research of Concern (DURC), including the role of institutional biosafety committees.
● Analyse the intellectual-property landscape of synthetic biology (patentability, open-source vs. proprietary models) and the opportunities and risks of the DIY Bio movement.
● Construct an integrated regulatory strategy for a synthetic biology product, situating it within a structured preclinical development plan, in coordination with the other two modules.