Cellular and Molecular Biology

ADVANCED MOLECULAR BIOLOGY (Biomolecular, Neurobiological)

ADVANCED MOLECULAR BIOLOGY

Academic year 2024/2025

Sommario del corso

• Course objectives
• Results of learning outcomes
• Program
• Course delivery
• Learning assessment methods
• Support activities
• Suggested readings and bibliography
• Notes
• Teaching tools
• Course card

Course objectives

This course contributes to the learning objectives included into the Master's program in Cellular and Molecular Biology (Biologia Cellulare e Molecolare).

The first objective is to develop the knowledge in the areas of genomics, epigenomics, transcriptomics and transcriptional and post-transcriptional regulatory networks. The second objective is to acquire the applicative abilities to comprehend scientific literature in the field, including the ability to dissect methodologies and approaches, and extract information from -omics and complex data.

Specific objectives are:

• Update basic molecular biology in the light of research approaches opened by the advent of high throughput genome sequencing technologies.
• Update regulatory biology, focusing on epigenomics, genomic programming and reprogramming, in addition to transcriptional and post-transcriptional regulation of gene expression. 
• Gain introductory understanding of gene interaction at the network and systems biology level.
• Ability to read and interpret research articles in the field of regulatory genomic molecular biology.
• Explore applications of -omics studies in different fields, focusing on molecular biology and neurobiology.

Results of learning outcomes

1. Knowledge and understanding:

Knowledge:

• Key analytical methods in genomics, epigenomics and transcriptomics.
• Transcriptional regulation in higher eukaryotes, including alternative RNA transcript generation, non-coding RNAs and associated functions.
• Mechanisms of global post-transcriptional gene expression regulation
• Constitutive principles of gene regulatory networks.
• Gene regulatory networks in developmental processes, with particular emphasis to neurobiology. 

Understanding:

• Understanding how a molecular biology study is planned and conducted.
• Understanding how results are presented and discussed in a primary scientific journal, and analyzing them within of "state-of-the-art".
• Selecting the best methodological approach to address a specific scientific question.
• Understanding the type of information that can be obtained from -omics studies, as well as the molecular mechanisms associated.  

2. Abilities:

• Conduct relevant literature searches on the course topics.
• Search for information on, and expose a summary of, the main methods of genomics and functional genomics.
• Analyze, interpret and report recent scientific studies concerning one of the course topics, including the methodology used.
• Interpret results and diagrams relating to the main issues discussed.
• Individuate which methods should be used to address a specific problem in the field.
• Reporting and expose concisely the topics of the course, as organized in basics, novelties and methodology.

Program

1. Genomics: sequencing genomes by NGS technologies. Features of genomes in higher eukaryotes. Mutation and repair, rates of spontaneous mutations. Repetitive and transposable elements. Sequence databases and genomic browsers.
2. Epigenomics. Chromatin components and functional states, nuclear topological organization, chromosomal territories, eu- and hetero-chromatin domains. Methodology to study the 3D genome. Genomic imprinting, monoallelic expression and chromatin dynamics during development.
3. Transcriptomics: the transcribed part of genomes. RNA-seq technologies. Classification of transcripts and mature RNAs. Coding and non-coding genes and transcripts. RNA isoforms and classification. Non-coding RNA classification and functions.
4. Regulation of gene transcription. Promoter types, CpG methylation, nucleosome positioning and PTMs. Mediators and co-regulators. Transcriptional activation, distinct steps of the transcription cycle and their regulation. Enhancer programming. Pioneer, tissue-specific and signal-dependent transcription factors. LncRNA role in transcriptional regulation and chromatin dynamics.
5. Post-transcriptional regulation: alternative splicing, regulatory factors and mechanisms. Stability, decay and intracellular localization of RNAs. MicroRNA, lncRNAs and transcriptional/post-transcriptional regulatory circuits.
6. Epigenetics in cell differentiation, neurobiology and neurodegeneration. 
7. Computational methods for -omics data mining. Machine learning applications in regulatory genomics and epigenomics. 

Course delivery

The course is structured in two parts. The first part comprises of 48 hours of face-to-face lectures equivalent to 6 CFU credits.  The second part consists of 24 hours dedicated to the presentation, reading and discussion of recent scientific results, corresponding to 3 CFU.

All lessons will be conducted in person.

Learning assessment methods

The exam is divived in three modules:

1. Oral presentation on a given selected scientific paper.

Grading will consider ability to understand, expose and interpret experimental results. Grading is out of 30. Time: approximately 1 h.

2. Short review of the same paper chosen for oral scientific presentation.

Grading will consider ability to understand, analyze and synthesize a scientific paper, as well as the ability to develop a scientific dissemination text. Detailed guidelines can be accessed on the Campusnet website, within the couse webpage. The work must be originally generated by the students, including the graphics, to be published on The Molecular Post website. Grading is out of 30. The deadline for submitting the review will be approximately one week after the oral discussion of the paper. 

3. Written Moodle exam consisting of 12 open-ended and/or multiple choice questions.

Grading will consider knowledge of material: slides, reviews/scientific papers discussed during course lectures. Grading is out of 30. Time: approximately 1 h. Before performing the test, students are required to read the Ethical Code: https://www.unito.it/sites/default/files/allegati/01-08-2014/cod_etico_comunita_universitaria.pdf. An English translation is available here: Code of Ethical Conduct.

The final grade is the weighted mean of the three single grades. A passing grade of 18/30 is required in all the modules to achive the final grade. In case of failure of one of the three modules, the student will need to retake the failed module,while the grade of the other modules will remain unchanged.

Support activities

If requested, in-person or online tutoring activities will be provided on specific topics covered in class and/or on the explanation of articles assigned for oral presentation and written short reviews.

The supplementary reading material consists on the papers and reviews utilized for the lectures slides. Following each lesson, along with the slides, references of papers and reviews utilized will be uploaded on Campusnet and Moodle websites corresponding to the course page. 

Notes

To effectively study proficiently advanced molecular biology, which is one of the fundamental courses in this Master, constant and continous participation, exercise and study are indispensabe. 

The knowledge acquired in Lesson N will be essential to understand Lesson N+1, whose content will be essential for understanding Lesson N+2, and so forth.

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