Biotechnologies

Activity type

Discipline biotecnologiche comuni

SSD

BIO/14

Year

3rd year

Semester

1st semester

CFU

6

Hours distribution

48 classroom hours

Lecturers

ALESSANDRA SEBASTIANA MAR CARUSO

Activity type

Discipline biotecnologiche comuni

SSD

BIO/10

Year

3rd year

Semester

1st semester

CFU

6

Hours distribution

40 classroom hours, 12 training hours

Lecturers

ALESSANDRO PAIARDINI

KNOWLEDGE AND UNDERSTANDING
The main goal of the course is to provide students with the tools necessary for a detailed and critique analysis of the structure of proteins and their macromolecular complexes using Bioinformatics. The first part of the course is dedicated to the theory of Bioinformatics algorithms. During the second part of the course, students are challenged with practical exercises on the structural analysis of protein models by means of open source software. The course consists of lectures that cover the main topics of the program and practical exercises. Exercises are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules. Beside textbooks, students have access to lectures' slides, scientific articles, and other teaching resources made available trough this web site.

APPLYING KNOWLEDGE AND UNDERSTANDING
The educational aim of the course is to achieve the necessary knowledge for a critical analysis of the structure of proteins and their interactions. By the end of the course students will have acquired the skills necessary to deal with the analysis and experimental study of biological macromolecules. They will learn how to retrieve protein and nucleic acid coordinates from the PDB database, recognize the fold and use software for a detailed analysis of their structure.

MAKING JUDGEMENTS
The course is aimed at increasing the ability to critically analyze the sequence and structure of proteins and other biological macromolecules.

COMMUNICATION SKILLS
The course includes significant activity of classroom discussion aimed at developing the ability of students to transfer skills acquired in support of their arguments. In the final exam, students must solve weblems and eventually take an oral presentation on the structure and function of an assigned protein.

LEARNING SKILLS
The many advancements of scientific research, particularly in the field of bioinformatics, biochemistry and molecular biology, require a constant updating. For this reason, the course aims to provide the necessary tools to achieve a wider knowledge and to align skills to the advancement in biology and bioinformatics research.

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1. Knowledge and understanding:
Students should demonstrate a thorough knowledge of the fundamental principles of bioinformatics, including concepts in molecular biology, genetics, and informatics. This entails an understanding of DNA, genomes, proteins, and their interactions, as well as sequencing techniques and biological data storage.

2. Applied knowledge and understanding:
Students should be able to utilize bioinformatics tools and resources for the analysis of biological data. This includes the ability to use specialized software for sequence alignment and annotation, identification of conserved motifs and regions, as well as analysis of gene expression and metabolic pathways.

3. Judgement autonomy:
Students should be capable of applying statistical methods and machine learning algorithms for the interpretation and analysis of biological data. This involves assessing the statistical significance of results, identifying patterns and correlations within the data, and employing classification and regression algorithms for processing biological information.

4. Communication skills:
Students should demonstrate proficiency in effectively communicating and presenting bioinformatics results. This includes the ability to interpret and convey analysis findings clearly and concisely, both in written and oral form, and to present information visually through graphs, tables, and diagrams.

5. Learning skills:
Students should possess the ability to independently acquire new knowledge and skills in the field of bioinformatics. This entails identifying and utilizing relevant information sources, developing effective learning strategies, and adapting to new technologies and advancements in the field of bioinformatics.

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Basic knowledge of Chemistry, Mathematics, Physics, Organic Chemistry, acquired in the courses of previous years.

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Introduction to bioinformatics; biological data
banks; sequence comparison with dot matrix; and dynamic algorithms; statistical
assessment of an alignment; scoring matrices; sequence data bank search;
multiple sequence alignment and principles of molecular phylogenesis; profile
search; motives; gene prediction; secondary structure and accessibility
prediction; structural evolution of proteins. Homology modeling and threading.
Structural evolution of proteins; Ab-initio protein structure prediction; molecular
mechanics; docking and pharmacoforic prediction; drug design; a programmino
language: Python.

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Stefano Pascarella, Alessandro Paiardini - Bioinformatica - Zanichelli, 2010

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https://elearning.uniroma1.it/course/view.php?id=4942

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The course consists of lessons and lectures that cover the main topics of the program, and practical sessions. Practical sessions are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules.

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Course attendance is not mandatory, but strongly recommended

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Final assessment: Exercises on PC + Oral exam

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Question 1:

How many scientific works have been published between 2000 and 2009, which contain the words acetylcholinesterase and structure in the title? How many of these are Reviews? What is depicted in Fig. 2 of the Review published by Silman I, Sussman JL. on this topic (include the legend of the figure)? What is the PDB code of the facility referred to in the figure, which contains the drug Donepezil (Aricept)? What is this drug used for? What are the coordinates of the first atom of the structure?

Question 2:

How many clinical trials have been published in 2011 and 2012, which contain as a medical topic item: “multiple sclerosis”? How many of these have the word "Alemtuzumab" in the title? What is the PDB code of the Alemtuzumab structure, resolved at 1.9Å? What is the co-crystallized antigenic sequence in this case? Which residuals interact with it (report type of residue, PDB file numbering and type of interaction).

Question 3:

How many clinical trials have been published in 2012, which contain as a medical topic: “multiple sclerosis”? How many of these have the word "BG-12" in the title? What molecule does this code refer to? What is its mechanism of action? How many PDB files contain this molecule as a ligand? How many total degrees of freedom does the molecule have?

Question 4:

How many clinical trials have been published in 2011 and 2012, which contain as a medical topic item: “tacrolimus”? What is the mechanism of action of tacrolimus and the protein target? How many PDB files contain this molecule as a ligand? In the structure published by Griffith et al., Which residues interact with it (report type of residue, numbering of the PDB file and type of interaction).

Question 5:

How many free full text reviews were published in 2011 and 2012, which contain rapamycin as a medical item? How many of these contain the word "sirolimus" in the title? What molecule does this term refer to? What is its mechanism of action? How many PDB files contain this molecule as a ligand? Among these, which code refers to the structure published by Fulton et al in 2006? What residues interact with rapamycin in this structure? (indicate type of residue, numbering of the PDB file and type of interaction).

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