509940 - RNA TECHNOLOGIES & PROTEIN ENGINEERING & SYSTEMS BIOLOGY

insegnamento

ID:

509940

Durata (ore):

88

CFU:

SSD:

Biologia molecolare

Anno:

2026

Periodo di attività

Primo Semestre (28/09/2026 - 15/01/2027)

Obiettivi Formativi

RNA Technologies:
At the end of the course, students will have acquired advanced, state-of-the-art concepts of modern RNA biology and high-throughput biotechnology. Specifically, they will learn:

Transcriptome-wide profiling technologies, variants of single-cell RNA sequencing and spatially resolved transcriptomics.
Post-transcriptional dynamics and translatome analysis, focusing on RNA-binding proteins and ribosome profiling.
Advanced in situ and single-molecule RNA methods, such as Proximity Ligation Assay (PLA)-based approaches, single-molecule RNA imaging/tracking, and in situ sequencing.
Protocol development and foundations on image analysis, through practical activities involving protocol design, assay workflow building, and analysis of imaging data.

Protein Engineering:
At the end of the course, students will have acquired the fundamental concepts of molecular biology applied to biotechnology. In particular, they will learn:

(1) In-depth knowledge of protein biochemistry.
(2) The most recent strategies for modifying protein structure/function.
(3) The ability to analyze a protein and predict potential interactions with other proteins;
(4) Principles of Protein Design.
(5) Experimental and theoretical Methodologies for 3D structural determination.

Prerequisiti

Knowledge of Biochemistry and Molecular Biology. Notions of Inorganic/organic chemistry. Basic concepts of RNA sequencing / Next-Generation Sequencing (NGS).

Metodi didattici

The course is structured through lectures and practical experiences in the laboratory.
Regarding the lectures, PowerPoint presentations are used, which will be made available to students in the dedicated section on the Moodle KIRO platform. Scientific articles referenced in the lectures will also be provided on the KIRO platform.
During the frontal lectures, we will aim to directly engage students for a more facile and intuitive learning experience using interactive tools.

During the laboratory sessions, students will be guided in the purification of recombinant proteins and in the growth of protein crystals for research purposes.
Participation in both the lectures and sessions is strongly recommended. Laboratory sessions are mandatory.
Attendance to lectures is strongly recommended; laboratory sessions are mandatory.

Verifica Apprendimento

RNA Technologies:
The examination will consist of a written/multiple choices exam covering the topics addressed during both the frontal lectures and the practical activities. Students will be evaluated on their critical understanding of RNA technologies, experimental design capabilities, and data interpretation skills. The same exam will include both questions from this course module and the Genes and genomes module (Dr. Valentina Serpieri).

Please note that the 2026-2027 course content differs from that of the 2025-2026 academic year. Therefore, students who attended the 2025-2026 courses may take the corresponding exams until December 2026. Beginning in 2027, all exams will be based exclusively on the 2026-2027 syllabus.
Protein Engineering:
The knowledge will be assessed through an oral exam. Students will be evaluated on how well they have integrated the knowledge acquired in the two modules, and a single grade will be recorded for the three modules.
NMR laboratory:
The assessment of this practical course will be based on participation in activities during the course and a final oral exam based on the covered topics. Each student will be given one practical task, and their problem-solving skill will be evaluated based on the versatility of their approach.

Testi

RNA Technologies:
State-of-the-art scientific reviews and research papers referencing foundational literature on RNA-seq, single-cell transcriptomics, ribosome profiling, the RNA-binding proteome, PLA technology, single-molecule RNA tracking, and spatial transcriptomics, in situ sequencing and the other topics covered during the classes and practical activities.

Protein Enginering:
Watson (et. al.), Biologia Molecolare del Gene, 2022.

Allison, Fondamenti di Biologia Molecolare, 2023, Zanichelli.
James Keeler. Understanding NMR Spectroscopy. WILEY.

State-of-the-art scientific papers

Contenuti

RNA Technologies:
Specific variants of Transcriptome Profiling and Bulk Technologies.
Overview on multiple methods of Single-Cell Transcriptomics.
Translatome and RNA-Protein Interactions
Methods based on proximity-ligation assasys
Single-molecule RNA imaging
Spatial Transcriptomics
In Situ RNA Sequencing
Optional (depending on the teaching progress): principles of multi-omics and RNA-based therapeutics

Laboratory and Practical Activities
Building an in situ sequencing protocol
Image analysis and group-work

Protein Engineering:
Introduction to proteins and protein domains
The modularity of proteins
Understanding Protein Folding
Mutations .vs. Functions
Traditional protein engineering
Protein Design
Experimental and theoretical 3D structural determination methods:
- X-ray Crystallography
- Cryo-electron microscopy
- NMR.
The NMR practical laboratory will be held by

Prof. Nasrollah Rezaie Ghaleh and it will cover:
•Basics of NMR theory;
•How NMR spectrometers work;
•How NMR spectra are collected and processed;
•How NMR peaks are assigned;
•How protein structures are determined based on NMR data;
•How protein dynamics are quantified based on NMR data;
•How protein interaction interfaces are mapped through NMR titration data.