Methods in Biotechnology
A.Y. 2021/2022
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
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
E-learning may be used, if required by the current legislation, to provide didactically innovative content (team work, journal club). In specific cases, asynchronous lessons may be made available.
Course syllabus
Section 1 Introduction
- fundamentals in genetics
- fundamentals in molecular biology
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.
- fundamentals in genetics
- fundamentals in molecular biology
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
PLEASE CHECK THE SYLLABUS PROVIDED IN THE MOODLE/ARIAL PAGE OF THE COURSE!!!
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.
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.
Teaching methods
Lectures: genomics 3,5 CFU; functional genomics 3 CFU
Workshops/practical experience: genomics 1.5CFU; functional genomics 1 CFU
Lectures and workshops are developed using IT platforms (MS Teams and MOODLE or ARIAL), or in the classroom. Experimental simulations will be conducted using specific software. Depending on the circumstances, an offsite training tour may be organized.
Workshops/practical experience: genomics 1.5CFU; functional genomics 1 CFU
Lectures and workshops are developed using IT platforms (MS Teams and MOODLE or ARIAL), or in the classroom. Experimental simulations will be conducted using specific software. Depending on the circumstances, an offsite training tour may be organized.
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; Bioinformatics and Functional Genomics, 3rd Edition Jonathan Pevsner ISBN: 978-1-118-58178-0 October 2015 Wiley-Blackwell 1168 Pages
Assessment methods and Criteria
1. evaluation of the teamwork developed 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 over the 30 available.
2. evaluation of acquired knowledge. After the end of the course, students take either a written or an oral exam. The written exam consists of 10 questions, in two hours. Each module contributes 5 questions. Of the ten questions, four are open and require the drafting of a short text. The other questions are closed and require ability to use the data and the knowledge acquired to solve problems. The oral exam can be taken independently for each module, with a timing that will be provided during the course and advertised in the MOODLE / ARIAL page. For both modules the oral exam consists of 6 open questions for a total of 30 minutes (the first question is free for the student to choose).
Specific procedures for students with disabilities or specific learning disabilities (DSA) will be applied also for telematic exams. Here the complete information:
https://www.unimi.it/en/study/student-services/services-students-disabilities
https://www.unimi.it/en/study/student-services/services-students-specific-learning-disabilities-sld
In case you need specific procedures, please inform the teacher by mail at least 10 days before the exam, including in the addresses [email protected] or [email protected].
2. evaluation of acquired knowledge. After the end of the course, students take either a written or an oral exam. The written exam consists of 10 questions, in two hours. Each module contributes 5 questions. Of the ten questions, four are open and require the drafting of a short text. The other questions are closed and require ability to use the data and the knowledge acquired to solve problems. The oral exam can be taken independently for each module, with a timing that will be provided during the course and advertised in the MOODLE / ARIAL page. For both modules the oral exam consists of 6 open questions for a total of 30 minutes (the first question is free for the student to choose).
Specific procedures for students with disabilities or specific learning disabilities (DSA) will be applied also for telematic exams. Here the complete information:
https://www.unimi.it/en/study/student-services/services-students-disabilities
https://www.unimi.it/en/study/student-services/services-students-specific-learning-disabilities-sld
In case you need specific procedures, please inform the teacher by mail at least 10 days before the exam, including in the addresses [email protected] or [email protected].
Functional genomics
AGR/07 - AGRICULTURAL GENETICS
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY
AGR/12 - PLANT PATHOLOGY
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY
AGR/12 - PLANT PATHOLOGY
Computer room practicals: 16 hours
Lessons: 24 hours
Lessons: 24 hours
Professor:
Pasquali Matias
Genomics
AGR/07 - AGRICULTURAL GENETICS
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY
AGR/12 - PLANT PATHOLOGY
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY
AGR/12 - PLANT PATHOLOGY
Computer room practicals: 16 hours
Practicals: 16 hours
Lessons: 8 hours
Practicals: 16 hours
Lessons: 8 hours
Professor:
Pozzi Carlo Massimo
Molecular taxonomy
AGR/07 - AGRICULTURAL GENETICS
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY
AGR/12 - PLANT PATHOLOGY
AGR/11 - GENERAL AND APPLIED ENTOMOLOGY
AGR/12 - PLANT PATHOLOGY
Computer room practicals: 32 hours
Lessons: 8 hours
Lessons: 8 hours
Professor:
Montagna Matteo
Professor(s)