Methods in biotechnology
A.Y. 2020/2021
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.
Lesson period: First semester (In case of multiple editions, please check the period, as it may vary)
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Most of the lessons are delivered synchronously via e-learning on the MSTeams (LINK: https://teams.microsoft.com/l/team/19%3ae5c2b2d475e046db956dea76a8bb0e5…) platform and recorded. Some particularly meaningful lessons are delivered in person. E-learning is also used to provide didactically innovative content (team work, journal club). In specific cases, asynchronous lessons (videolessons consisting of recording the teacher's desktop with audio commentary) of synthetic duration will be made available.
The methods and criteria for participating in face-to-face lessons, which require a reservation with a special app, will be published in time on the pages
Ariel of teaching, as well as all the teaching materials and notices relating to any update related to the evolution of the legislation imposed by Covid-19.
The methods and criteria for participating in face-to-face lessons, which require a reservation with a special app, will be published in time on the pages
Ariel of teaching, as well as all the teaching materials and notices relating to any update related to the evolution of the legislation imposed by Covid-19.
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.
- 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.
These topics, for example, are a useful wealth of knowledge: Plant cell, haploid-diploid development cycle of higher plants, mitosis and meiosis
Chemical composition and structure of DNA, the Watson and Crick model, DNA replication, gene structure of a eukaryote, transcription, translation, genetic code, expression regulation, dogma of molecular biology
Mutations, molecular basis of mutations, point mutations, IN / DEL, gene mutations, chromosomal.
Polyploidy, auto and allopolyploidy. Causes and mechanisms of origin, advantages of polyploidy. Importance in domestication, diffusion.
Mendel, theory and practice of Classical Mendelian Genetics, inheritance of simple characters, Mendel's three laws, Chi2 test
Chromosomal theory of inheritance
Dominance, semi-dominance (partial dominance), co-dominance. Meaning in allogamic and autogamous species. Genetic load in genetic species and purifying selection in autogamous species. Allard hypothesis
Gene interaction or epistasis and pleiotropy.
Gene association and recombination, crossing over, recombination, calculation of map distances between loci, genetic maps, linkage.
Transition from gene markers to molecular markers. Genetic and molecular markers, concepts, types (RFLP, SSR, SNP, IN / DEL) and their use, PCR, genome sequencing, genomic databases, outline of Next Generation Sequencing
Gene haplotypes at the causal loci of natural gene variability and haplotypes with diagnostic molecular markers.
Quantitative or complex traits, normal distribution: multifactorial hypothesis, genetic control of quantitative traits. QTL: loci for quantitative characters.
Heterosis.
Basics of the genetic improvement of autogamous and allogamic plants and selection assisted by molecular markers.
These topics, for example, are a useful wealth of knowledge: Plant cell, haploid-diploid development cycle of higher plants, mitosis and meiosis
Chemical composition and structure of DNA, the Watson and Crick model, DNA replication, gene structure of a eukaryote, transcription, translation, genetic code, expression regulation, dogma of molecular biology
Mutations, molecular basis of mutations, point mutations, IN / DEL, gene mutations, chromosomal.
Polyploidy, auto and allopolyploidy. Causes and mechanisms of origin, advantages of polyploidy. Importance in domestication, diffusion.
Mendel, theory and practice of Classical Mendelian Genetics, inheritance of simple characters, Mendel's three laws, Chi2 test
Chromosomal theory of inheritance
Dominance, semi-dominance (partial dominance), co-dominance. Meaning in allogamic and autogamous species. Genetic load in genetic species and purifying selection in autogamous species. Allard hypothesis
Gene interaction or epistasis and pleiotropy.
Gene association and recombination, crossing over, recombination, calculation of map distances between loci, genetic maps, linkage.
Transition from gene markers to molecular markers. Genetic and molecular markers, concepts, types (RFLP, SSR, SNP, IN / DEL) and their use, PCR, genome sequencing, genomic databases, outline of Next Generation Sequencing
Gene haplotypes at the causal loci of natural gene variability and haplotypes with diagnostic molecular markers.
Quantitative or complex traits, normal distribution: multifactorial hypothesis, genetic control of quantitative traits. QTL: loci for quantitative characters.
Heterosis.
Basics of the genetic improvement of autogamous and allogamic plants and selection assisted by molecular markers.
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.
Teaching Resources
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
Assessment methods and Criteria
1. evaluation of the work developed in team during each of the course modules. Students will actively participate in the realization of team workshops and / or the presentation of scientific articles, where they will have to demonstrate their ability to interpret data and plan experiments. Both the contribution of individuals and the work of the team are evaluated. These activities can lead to a total of 2 points for each module (i.e. 6 points in total).
2. evaluation of acquired knowledge. After the end of the course, students take a written exam in the classroom (divided into cohorts), consisting of 15 questions, in two hours. Each module contributes 5 questions. Of these, two are open and require the drafting of a short text, also structured in points. The other questions are closed and require ability to use the data and knowledge acquired to solve problems.
2. evaluation of acquired knowledge. After the end of the course, students take a written exam in the classroom (divided into cohorts), consisting of 15 questions, in two hours. Each module contributes 5 questions. Of these, two are open and require the drafting of a short text, also structured in points. The other questions are closed and require ability to use the data and knowledge acquired to solve problems.
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
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY - University credits: 0
AGR/12 - PLANT PATHOLOGY - University credits: 0
Computer room practicals: 16 hours
Lessons: 24 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
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY - University credits: 0
AGR/12 - PLANT PATHOLOGY - University credits: 0
Practicals: 32 hours
Lessons: 8 hours
Lessons: 8 hours
Professor:
Pozzi Carlo Massimo
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
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
Laboratories: 16 hours
Lessons: 8 hours
Professor:
Montagna Matteo
Educational website(s)
Professor(s)
Reception:
Tuesday 8:00 - 12:00 am, appointment needed
Via Celoria, 2 - Edificio 21070 - second floor, office 2010