Genetics and Molecular Biology

Next Generation Sequencing: methodologies and applications (Lectures 1-13, 26 h) Methodologies • History of DNA sequencing • Human Genome Project • Next Generation Sequencing (deep sequencing) • NGS Platforms and technologies • Third Generation Sequencing Applications • GENOMICS • Whole Genome Sequencing (WGS) • Whole Exome Sequencing (WES) • TRANSCRIPTOMICS • RNA-seq • EPIGENOMICS • ChIP-seq • MNAse-seq • DNase-seq • Bisulfite-seq etc. • Metagenomics and microbiomics • Towards precision medicine • NGS data analysis • Single cell sequencing Single Molecule Techniques and Super Microscopy (Lectures 14-16, 6 h) Studying single molecules • AFM (Atomic Force Microscopy) • Optical Tweezers and Magnetic Tweezers • Single molecule FRET From Microscopy to Nanoscopy: beyond the limits of Abbe law • STED (Stimulated Emission Depletion) • STORM (Stochastic Optical Reconstruction Microscopy) Advanced Tools to Target and Edit Genomes (Lectures 17-20, 8h; Flipped learning, 2 h; Laboratory Exercise, 12 h) • Gene targeting by site-specific nucleases: ZFNs (Zinc Finger Nucleases), TALENs (transcription activator-like effector nucleases) • CRISPR/CAS revolution: a simple and powerful method to edit genomes • Applications of the CRISPR/CAS system • Future perspectives of gene and genome editing • Design a project to target a gene by CRISPR/Cas9 (Flipped learning) • Cloning single-guide RNA expressing vectors (Lab exercise)

Knowledge of English Basic notions of Molecular Biology

There is not a specific textbook for the course. Knowledge of basic biomolecular techniques is expected to succeed in the course. Reviews and articles, together with lectures (PDF), will be available on the course website on e-learning platform TEXTS Basic knowledge Wilson and Walker’s Principles and Techniques of Biochemistry and Molecular Biology (8th edition) – Hofmann A & Clokie S, Cambridge University Press (2018) Biotecnologie Molecolari, principi e tecniche (2a edizione) – Brown TA, Zanichelli 2017 Gene Cloning and DNA Analysis: An Introduction (7th edition) - Brown TA, Wiley & Sons (2016) Biologia Molecolare del Gene (settima edizione) (cap. 7; parte 6, Appendix) – Watson et al., Zanichelli ed. From Genes to Genomes – Dale JW, Von Schantz M, Plant N, Wiley-Blackwell eds.* Biologia Molecolare - Zlatanova J and van Holde KJ, Zanichelli ed. Specific knowledge Reviews and articles (available on the course website) Next-Generation DNA Sequencing Informatics – Brown, CSHL press# Atomic Force Microscopy For Biologists – Morris et al., Imperial College Press# * Available at the Department library (Antropologia) # Available at the teacher’s room (Fisiologia Generale, 1° floor, Room 10)

Lectures and lab practice

40 hours of face-to-face lectures (20 lectures) and 12 hours of lab practice (on three days)

Students will be evaluated by oral exam. Students have the opportunity to present a research project on a task regarding gene editing. This will be evaluatd as part of the exam

Lectures and lab practice

Next Generation Sequencing: methodologies and applications (Lectures 1-13, 26 h) Methodologies • History of DNA sequencing • Human Genome Project • Next Generation Sequencing (deep sequencing) • NGS Platforms and technologies • Third Generation Sequencing Applications • GENOMICS • Whole Genome Sequencing (WGS) • Whole Exome Sequencing (WES) • TRANSCRIPTOMICS • RNA-seq • EPIGENOMICS • ChIP-seq • MNAse-seq • DNase-seq • Bisulfite-seq etc. • Metagenomics and microbiomics • Towards precision medicine • NGS data analysis • Single cell sequencing Single Molecule Techniques and Super Microscopy (Lectures 14-16, 6 h) Studying single molecules • AFM (Atomic Force Microscopy) • Optical Tweezers and Magnetic Tweezers • Single molecule FRET From Microscopy to Nanoscopy: beyond the limits of Abbe law • STED (Stimulated Emission Depletion) • STORM (Stochastic Optical Reconstruction Microscopy) Advanced Tools to Target and Edit Genomes (Lectures 17-20, 8h; Flipped learning, 2 h; Laboratory Exercise, 12 h) • Gene targeting by site-specific nucleases: ZFNs (Zinc Finger Nucleases), TALENs (transcription activator-like effector nucleases) • CRISPR/CAS revolution: a simple and powerful method to edit genomes • Applications of the CRISPR/CAS system • Future perspectives of gene and genome editing • Design a project to target a gene by CRISPR/Cas9 (Flipped learning) • Cloning single-guide RNA expressing vectors (Lab exercise)

Knowledge of English Basic notions of Molecular Biology

There is not a specific textbook for the course. Knowledge of basic biomolecular techniques is expected to succeed in the course. Reviews and articles, together with lectures (PDF), will be available on the course website on e-learning platform TEXTS Basic knowledge Wilson and Walker’s Principles and Techniques of Biochemistry and Molecular Biology (8th edition) – Hofmann A & Clokie S, Cambridge University Press (2018) Biotecnologie Molecolari, principi e tecniche (2a edizione) – Brown TA, Zanichelli 2017 Gene Cloning and DNA Analysis: An Introduction (7th edition) - Brown TA, Wiley & Sons (2016) Biologia Molecolare del Gene (settima edizione) (cap. 7; parte 6, Appendix) – Watson et al., Zanichelli ed. From Genes to Genomes – Dale JW, Von Schantz M, Plant N, Wiley-Blackwell eds.* Biologia Molecolare - Zlatanova J and van Holde KJ, Zanichelli ed. Specific knowledge Reviews and articles (available on the course website) Next-Generation DNA Sequencing Informatics – Brown, CSHL press# Atomic Force Microscopy For Biologists – Morris et al., Imperial College Press# * Available at the Department library (Antropologia) # Available at the teacher’s room (Fisiologia Generale, 1° floor, Room 10)

Lectures and lab practice

40 hours of face-to-face lectures (20 lectures) and 12 hours of lab practice (on three days)

Students will be evaluated by oral exam. Students have the opportunity to present a research project on a task regarding gene editing. This will be evaluatd as part of the exam

Lectures and lab practice