First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
EVOLUTIONARY BIOLOGY
Course unit
MOLECULAR METHODS AND BIOINFORMATICS
SCP8084938, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2019/20

Information on the course unit
Degree course Second cycle degree in
EVOLUTIONARY BIOLOGY
SC1179, Degree course structure A.Y. 2018/19, A.Y. 2019/20
N0
bring this page
with you
Number of ECTS credits allocated 11.0
Type of assessment Mark
Course unit English denomination MOLECULAR METHODS AND BIOINFORMATICS
Website of the academic structure http://biologia.scienze.unipd.it/2019/laurea_magistrale_biologiaevoluzionistica
Department of reference Department of Biology
E-Learning website https://elearning.unipd.it/biologia/course/view.php?idnumber=2019-SC1179-000ZZ-2019-SCP8084938-N0
Mandatory attendance
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge GIANLUCA OCCHI BIO/13
Other lecturers STEFANIA BORTOLUZZI BIO/13

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/13 Applied Biology 4.0
Other -- -- 4.0
Core courses BIO/11 Molecular Biology 3.0

Course unit organization
Period First semester
Year 1st Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Practice 2.0 32 18.0 No turn
Laboratory 2.0 32 18.0 No turn
Lecture 7.0 56 119.0 No turn

Calendar
Start of activities 30/09/2019
End of activities 18/01/2020
Show course schedule 2019/20 Reg.2018 course timetable

Examination board
Board From To Members of the board
2 METODI MOLECOLARI E BIOINFORMATICA 2019-2020 01/10/2019 27/11/2020 OCCHI GIANLUCA (Presidente)
BORTOLUZZI STEFANIA (Membro Effettivo)
COPPE ALESSANDRO (Supplente)
1 METODI MOLECOLARI E BIOINFORMATICA 2018-2019 01/10/2018 30/11/2019 BORTOLUZZI STEFANIA (Presidente)
OCCHI GIANLUCA (Membro Effettivo)
COPPE ALESSANDRO (Supplente)

Syllabus
Prerequisites: Basic knowledge of genetics and molecular biology will help in the understanding of the biological motivations of bioinformatics. Basic skills in computer science.
Target skills and knowledge: The course will give medium-advanced skills on the main topics in the fields of biotechnologies with particular attention to the DNA recombinant technologies and their fields of application – e.g. animal/vegetal transgenesis, genome editing – and in all the classic topics of bioinformatics, covering databases and data retrieval, sequence alignments and similarity searches, structure predictions, and NGS applications to genomics and transcriptomics.
Globally, the course will give to students basic but up-to-date knowledge and skills useful for comprehension and development of studies in the evolutionary biology field.
Examination methods: Written final exam, with a separate test for each part of the the course. The test will contain multiple choice questions, as well as exercises and open-ended questions.
Each practical session will be evaluated.
The Journal Club will be also scored.
Assessment criteria: In their final examination the students should demonstrate understanding of the field and master the research methods, integrating the subjects of this course with other knowledge.
Evaluation criteria will be:
Understanding of course topics;
Critical thinking and ability to establish links between the topics;
Depth of acquired knowledge;
Ability to synthesize;
Correctness of scientific language.
Course unit contents: Molecular methods

- Basic methods in DNA manipulation.
- Defining goals of cloning experiments and designing of cloning strategies using specific vectors (e.g. plasmid and bacteriophage).
- Principles and Applications of the Polymerase Chain Reaction.
- Mutagenesis techniques.
- Overview of the main blotting techniques and their applications.
- Methods for manipulate living organisms.
- Introduction to methods and tools for functional and structural analysis of the genes.
- Principles and Applications of genome editing

Bioinformatics

- Database e data retrieval.
Algorithms for pairwise alignments, substitution matrices. Similarity searches.
Multiple alignments: progressive (Clustal Omega) and consistency-based (Tcoffee) methods.
Biomolecule structure prediction: secondary structure prediction and protein folding (ab inizio, comparative modeling, threading).
Genomics resources (NCBI, UCSC Genome Browser, ENSEMBL).
Genome sequencing, assembly, and annotation; Genome resequencing.
Introduction to RNA-seq data analysis.
Practical sessions using Shell and Python programming.
Planned learning activities and teaching methods: The course will include lectures and practicals.
The teachers will encourage involvement of students by interactive lessons, organization of group work, Journal Club (Molecular Methods and Bioinformatics applied in Comparative Genomics and Molecular Evolution), discussion and periodical evaluation of students during practical sessions.
The course materials (lecture supports, guides and data for practical sessions) will be included in a dedicated web site (http://compgen.bio.unipd.it/~stefania/Didattica/).
Other file sharing and collaborative working tools (e.g. using Google tools) will be also implemented.
Additional notes about suggested reading: Additional course materials will be online and/or shared with students.
Textbooks (and optional supplementary readings)
  • Stefano Pascarella e Alessandro Paiardini., Bioinformatica. Dalla sequenza alla struttura delle proteine. --: Zanichelli, 2014. Parte di Bioinformatica Cerca nel catalogo
  • Jeremy W. Dale, Malcolm von Schantz, Nick Plant, Dai geni ai genomi: principi e applicazioni della tecnologia del DNA ricombinante.. --: EdiSES, 2013. Parte di Metodi Molecolari Cerca nel catalogo
  • Terry A. Brown., Biotecnologie molecolari principi e tecniche. --: Zanichelli, 2017. Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Active quizzes for Concept Verification Tests and class discussions

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)

Sustainable Development Goals (SDGs)
Good Health and Well-Being Quality Education