Methods in biotechnology

A.Y. 2019/2020
10
Max ECTS
120
Overall hours
SSD
AGR/07 AGR/11 AGR/12
Language
English
Learning objectives
The course is subdivided in 3 modules. The goal is to acquire knowledge and operational competencies in genomics, functional genomics and applications to plant improvement and to molecular taxonomy.
Expected learning outcomes
The student will acquire competencies in generating and analyzing data through the genomics and functional-genomics techniques. The student will be able to plan experiments using genomic sequencing, gene expression analyses, and their integration with metabolomics and proteomics. The student will be able to understand and apply knowledge in molecular taxonomy.
Course syllabus and organization

Unique edition

Responsible
Lesson period
First semester
Course syllabus
Section 1 Molecular taxonomy.
- Applications of molecular taxonomy from agri-food security to biodiversity and biomonitoring;
- Principles and methods of molecular taxonomy;
- DNA extraction from agri-food and other environmental matrices;
- DNA barcoding and metabarcoding: from single organism to communities;
- NGS sequences platform used in metabarcoding;
- Single marker vs multiple markers, PCR-free gene capture approaches;
- Reference databases and ad-hoc built databases;
- Workshops will be conducted on experimental design, primer selection and library preparation,
basic skills on bash environments, analyses of NGS data and taxonomy assignment

Section 2- Genomics.
- Techniques and approaches in genome, exome and epigenome sequencing;
- Strategies for plant genome analysis and assembly;
- Plant genome structure, synteny and evolution;
- Applications of genomics in plant breeding;
- Workshops will be conducted on sequence analysis and alignments; design of experiments in plant genomics;

Section 3 Functional genomics.
- Techniques and approaches in RNA analysis and modulation;
- Strategies for genome modification;
- Integration of high throughput /content techniques (omics) and data analysis;
- Workshops will be conducted on gene targeting; RNA expression analysis and integrated omics to modulate biological functions.
Prerequisites for admission
The student can take full advantage of the teachings if some background is known about molecular biology, molecular genetics (molecular markers and their use), organic chemistry, and biochemistry.
Teaching methods
5 CFU lesson (genomics 2CFU; functional genomics 2CFU; molecular taxonomy 1CFU); 5CFU practical lesson (genomics 1.5CFU; functional genomics 1.5; molecular taxonomy 2 CFU). Lectures and workshops, using IT platforms. Experimental simulations. Depending on the interaction with the students, an offsite training tour may be offered.
Bibliography
The slides (in English) will be timely provided during the course and will include explanatory text; additionally, papers and books abstracts will be posted on the Ariel website of the course. Suggested text books:-Genomes (T.A. Brown, 2018); Molecular Plant Taxonomy - Methods and Protocols. Ed. Pascale Besse. Humana Press, 2014.-Environmental DNA for biodiversity research and monitoring. P. Taberlet, A. Bonin, L. Zinger, E. Coissac. Oxford University Press, 2018
Assessement methods and criteria
The student is offered the opportunity to take the exam in oral form. The oral exam will include the presentation (15 minutes) of a scientific paper (or papers) broadly spanning the entire program. Additional 15 minutes will be devoted to 3 questions concerning the entire program. Alternatively, the student can take an oral exam composed of 4 questions about each of the main areas of the program (for a total of 12 questions).
Functional genomics
AGR/07 - AGRICULTURAL GENETICS - University credits: 0
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY - University credits: 0
AGR/12 - PLANT PATHOLOGY - University credits: 0
Practicals: 8 hours
Laboratories: 8 hours
Lessons: 24 hours
Professor: Pasquali Matias
Genomics
AGR/07 - AGRICULTURAL GENETICS - University credits: 0
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY - University credits: 0
AGR/12 - PLANT PATHOLOGY - University credits: 0
Practicals: 32 hours
Lessons: 8 hours
Molecular taxonomy
AGR/07 - AGRICULTURAL GENETICS - University credits: 0
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY - University credits: 0
AGR/12 - PLANT PATHOLOGY - University credits: 0
Practicals: 16 hours
Laboratories: 16 hours
Lessons: 8 hours
Educational website(s)
Professor(s)
Reception:
Tuesday 9:00 - 12:00 am, appointment needed
Via Celoria, 2 - Edificio 21070 - second floor, office 2010