Medical Biotechnology

Activity type

Medicina di laboratorio e diagnostica

SSD

MED/46

Year

1st year

Semester

1st semester

CFU

1

Hours distribution

8 classroom hours

Lecturers

DOMENICO RAIMONDO

Activity type

Discipline biotecnologiche comuni

SSD

BIO/13

Year

1st year

Semester

1st semester

CFU

5

Hours distribution

40 classroom hours

Lecturers

ALESSANDRA MARCHETTI

The course aims to provide knowledge of i) the molecular mechanisms controlling physiological cellular functions (e.g., cell proliferation, death, senescence, differentiation), ii) how the cell regulates these functions in response to stimuli from the tissue microenvironment, iii) how it integrates these signals in order to contribute to the tissue homeostasis, iv) the alterations found in different physio-pathological conditions. The neoplastic transformation will be used as a paradigm of deregulations involving multi-level cellular function, and the liver as example of organ for physio-pathological studies. The student, once acquired knowledge of the mechanisms that regulate cell functions, will acquire skills to propose experimental approaches for the analysis of these functions both in vitro and in vivo.
These skills will be developed through simulations of scientific problems in interactive lessons, where students will develop critical skills, will apply the acquired knowledge and will discuss collectively the possible experimental approaches for their solving.
Biocomuputing module:
To acquire proficiency in using the Unix shell as a fundamental tool for automating repetitive tasks and efficiently managing complex workflows. Students will learn how to combine commands to build operational pipelines and apply shell usage to advanced data processing tasks, with a particular focus on applications in high-performance computing (HPC) and bioinformatics analysis.

Students will acquire knowledge of the molecular mechanisms controlling normal cellular functions, of how cells regulate and integrate these functions in response to stimuli from tissue microenvironment, and their alterations in pathophysiological conditions. They will also acquire the skills to propose experimental approaches for analyzing these functions both in vitro and in vivo.
In addition, the student will acquire skills in the use of the Unix shell for the automation of repetitive tasks, data processing, and bioinformatics analysis.

Students must possess the following basic knowledge: - structure of prokaryotic and eukaryotic cells - mechanisms of cell division and DNA replication - mechanisms of transcription and translation processes - basic mechanisms regulating gene expression - fundamentals of genetics - structure and functions of biological macromolecules - basic techniques of genetic engineering - cell signaling

Module: Molecular bases of cellular functions I
N/D
Module: Biiocomputing
The Course is composed by the following units and topics:
1. Molecular mechanisms controlling the G1/S and G2/M transitions, mitosis and cytokinesis. Cell cycle inhibitors. Mitotic and DNA damage checkpoints. Molecular control of cell differentiation (e.g. muscle and hepatic cell differentiation). Mechanisms regulating cell proliferation, differentiation and quiescence. Methods for the study of cell cycle (6 hours).
2. Signal transduction from soluble factors and cell-cell/ECM-cell adhesions. Specificity of receptors for growth factors. Signal integration and methods for the study of signal transduction. Transduction of mechanical stimuli. (4 hours).
3. Molecular mechanisms and physio-pathological roles of the epithelial-to-mesenchymal transition (EMT). Inducers and molecular mediators. Genetic and epigenetic control of EMT (2 hours).
4. Cell senescence. Phenotypic, biochemical and molecular aspects. Mechanisms driving replicative and premature senescence. Senescence and tumors. Senescence and aging. Methods for the study of senescence (2 hours).
5. Mechanisms and physio-pathological roles of programmed cell death (apoptosis, necroptosis and pyroptosis). Phenotypic, biochemical and molecular aspects of the different types of cell death. Main methodologies for the study of cell death (4 hours).
6. Molecular mechanisms and physio-pathological roles of autophagy. Methods for the study of autophagy (2 hours).
7. Molecular mechanisms and functions of endoplasmic reticulum stress (ER stress) and signal transduction pathway called "unfolded protein response (UPR)". Physiological and pathological role. Crosstalk between ER stress, autophagy and cell death (2 hours).
8. Mechanisms controlling inter-cellular communication: microvesicles and exosomes. Diagnostic and therapeutic applications for the study of human diseases (2 hours).
9. Control of cellular functions in liver physiology and pathology (2 hours)
10. Loss of normal control mechanisms in cancer cells: molecular mechanisms and analysis of possible therapeutic approaches. Crosstalk between the tissue microenvironment and cancer cells (2 hours).
11. Basic molecular mechanisms for the regulation of cell functions:
- Functional regulations of proteins: regulation of protein-protein interactions, post-translational modifications, subcellular localization (1 hour)
- Protein degradation processes: general aspects, molecular mechanisms and functions. Role of the lysosome and the proteasome (1 hour)
- Epigenetic regulation of gene expression. Non-coding RNAs (microRNAs and lncRNAs): mechanism of action and functions. Methods for the study of epigenetic modifications (4 hours)

Furthermore, the following activities are planned (6 hours):
- Analysis of a scientific project with discussion in the classroom.
- Focus on technological tools for the study of cellular functions: proteomics (technologies and applications); flow cytometry and FACS (principles and applications)

Module: Molecular bases of cellular functions I
Teaching material, provided by the lecturer


Module: Biiocomputing
The teaching material, provided by the lecturer, include recent research articles and reviews, published in international journals, and the educational-informatic material utilized during lessons (slides, videos, tutorials).
It is recommended to refer to a basic cell biology textbook such as:
- Alberts et al., “L'essenziale della biologia molecolare della cellula" - Zanichelli ed.
- Hardin, Bertoni - "Becker. il mondo della cellula" - Pearson ed.

Module: Molecular bases of cellular functions I
N/D
Module: Biiocomputing
N/D

Teaching is organized through lectures, exercises, in-depth seminars, and interactive lessons involving the simulation of scientific project implementation.
The Biocomputing module consists of theoretical lessons and/or computer-based sessions

Mandatory attendance of at least 67% of lessons

For the BMFC module, the exam consists of a written test with open-ended questions, designed to assess the student's ability to solve scientific problems related to the topics covered in the course, applying the technologies learned. This is followed by an oral examination to further evaluate the knowledge acquired.
For the Biocomputing module, assessment will be based on the resolution of simple questions related to the course content, using the R software.
The final grade will reflect the student's ability to reason and apply the knowledge acquired, as demonstrated in both assessments.

1. Describe the functional significance of autophagy in cellular physiology
2. Describe the molecular mechanisms that regulate the induction of cellular senescence
3. Explain the experimental approaches used to identify apoptotic cell death

Module: Molecular bases of cellular functions I



Module: Biiocomputing

• Molecular mechanisms controlling cell cycle and differentiation-I


• Molecular mechanisms controlling cell cycle and differentiation-II


• Cell cycle checkpoints


• Signal transduction


• Cell senescence


• Epigenetic regulation of gene expression


• ncRNA:


• Mechanisms controlling inter-cellular communication: microvesicles and exosomes. 


• Apoptosis


• Necroptosis


• Piroptosis


• ER stress and UPR response


• Protein degradation. The ubiquitin-proteasome system


• Autophagy


• Neoplastic transformation


• Proteomics: