Methods in biotechnology
A.A. 2024/2025
Obiettivi formativi
The course is divided into 2 teaching units. A general introduction will allow the student to gather sufficient knowledge in genetics and molecular biology to be able to understand the scientific content of the two modules. The goal of the course is to acquire knowledge and operational competencies in genomics, functional genomics and applications to plant improvement. More in detail, the genomics module will provide knowledge in sequencing technologies, genome analysis, and their applications to plant breeding with focus on sustainability objectives. The functional genomics module will provide knowledge on RNA biology, methods for studying the transcriptome and integration of omics approaches to infer gene function.
Risultati apprendimento attesi
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. More in details, the student will be able to design a positional cloning mapping experiment, and to analyze genomics data using one or more benchmark software for genome wide analyses. The student will be able to interpret transcriptomic experiments, design and analyse qPCR experiment for validation of transcriptomic data and use databases with valuable functional genomics information. The student will learn practically how to work with RNA.
Periodo: Primo semestre
Modalità di valutazione: Esame
Giudizio di valutazione: voto verbalizzato in trentesimi
Corso singolo
Questo insegnamento può essere seguito come corso singolo.
Programma e organizzazione didattica
Edizione unica
Responsabile
Periodo
Primo semestre
Programma
o Introduction to genetics (basics concepts in formal genetics) (1 CFU)
o QTLs and their importance in breeding (1CFU)
-Basics in population genetics
-Mapping monogenic and polygenic traits
o DNA sequencing: from first to third generation and beyond (1 CFU)
-Extracting the information contained in the DNA: reading and annotating the sequences
-Exploiting the information contained in the DNA: comparative genomics
-Sequencing the epigenome and resequencing the genome
o Molecular Plant breeding basics (2 CFU)
-Molecular markers at work: marker assisted selection
-Using genomics for gene discovery: from positional cloning to forward/reverse genetics
-Workshop on positional cloning and candidate gene
-From cross-based to genome-based mapping: linkage disequilibrium, genome wide association studies, population structure
-Workshop on LD
o Genes in their working context: gene expression and functional genomics (3,5 CFU)
-Techniques and approaches in RNA analysis (spatial and temporal assessment)
-Strategies for genome modification
-Integration of high throughput /content techniques (omics) and data analysis for gene function and cell modifications
o 0,5 CFUs will be dedicated to laboratory actvities using RNA
o QTLs and their importance in breeding (1CFU)
-Basics in population genetics
-Mapping monogenic and polygenic traits
o DNA sequencing: from first to third generation and beyond (1 CFU)
-Extracting the information contained in the DNA: reading and annotating the sequences
-Exploiting the information contained in the DNA: comparative genomics
-Sequencing the epigenome and resequencing the genome
o Molecular Plant breeding basics (2 CFU)
-Molecular markers at work: marker assisted selection
-Using genomics for gene discovery: from positional cloning to forward/reverse genetics
-Workshop on positional cloning and candidate gene
-From cross-based to genome-based mapping: linkage disequilibrium, genome wide association studies, population structure
-Workshop on LD
o Genes in their working context: gene expression and functional genomics (3,5 CFU)
-Techniques and approaches in RNA analysis (spatial and temporal assessment)
-Strategies for genome modification
-Integration of high throughput /content techniques (omics) and data analysis for gene function and cell modifications
o 0,5 CFUs will be dedicated to laboratory actvities using RNA
Prerequisiti
PLEASE CHECK THE SYLLABUS OF THE COURSE ON THE MyAriel PAGE!!!!!
In order to best understand the content of this course, you should have basics in:
1. Mendelian and formal genetics (i.e. the genetics you had at the High School or during the BA; in case you did not have any genetics, please contact the teacher BEFORE the course)
2. DNA and gene structure
3. Recombination and its use in molecular mapping (i.e. what is a molecular map where traits/genes are distributed)
4. Molecular markers (i.e. a basic understanding of what a molecular marker is)
5. Basics in nucleic acids sequencing (i.e. what does it mean to sequence a DNA molecule)
6. Basics in plant breeding (i.e. what is plant breeding, and what are its goals)
8. Basics in molecular biology (plasmids, cloning techniques and strategies, bacterial and eukaryotes transformation, restriction enzymes and their use in molecular biology, DNA labeling, nucleic acid analysis)
9. Basics in cell biology
10. Basics in PC use
In order to best understand the content of this course, you should have basics in:
1. Mendelian and formal genetics (i.e. the genetics you had at the High School or during the BA; in case you did not have any genetics, please contact the teacher BEFORE the course)
2. DNA and gene structure
3. Recombination and its use in molecular mapping (i.e. what is a molecular map where traits/genes are distributed)
4. Molecular markers (i.e. a basic understanding of what a molecular marker is)
5. Basics in nucleic acids sequencing (i.e. what does it mean to sequence a DNA molecule)
6. Basics in plant breeding (i.e. what is plant breeding, and what are its goals)
8. Basics in molecular biology (plasmids, cloning techniques and strategies, bacterial and eukaryotes transformation, restriction enzymes and their use in molecular biology, DNA labeling, nucleic acid analysis)
9. Basics in cell biology
10. Basics in PC use
Metodi didattici
Lectures; active learning; interactive didactic workshops; didactic trip
Materiale di riferimento
Pdf, annotated files of the lectures, available on MyAriel platform; papers and textbooks and videos (provided by the teacher and made available on MyAriel), additional online resources made available through the slides.
Modalità di verifica dell’apprendimento e criteri di valutazione
The student may take a written or an oral exam.
The student may take the written exam in two forms: 1. After the end of the course, in the classroom consisting of 10 questions, in two hours. Each module of the course contributes 5 questions. Of these, two are open and require the drafting of a short text. The other 3 questions are closed and require ability to use the data and knowledge acquired to solve problems. 2. Intermediate written exams: one for Genomics (mid way during the course, during the didactic pause) and one for Functional genomics (end of course) [in this order]. The second option is offered only to the students of the current academic year. You need to pass the first one to access the second one. You need to pass both to pass it. Each exam of option 2 consists of 5 questions (open and/or closed), in 90 minutes.
Oral exam: students can take an oral exam for each of the two modules. Oral exam is composed of 5+5 questions (5 for each module) in 30 minutes (for each module). The first question of the Genomics module is the first question is at the student's discretion. Oral exams are upon appointment, independently for each module. The students are evaluated based on their knowledge of the tested topics, their capacity of leading an exposition of a topic for about 5 minutes, their capacity of connecting topics pertaining to different areas of the study subject. Furthermore, the exam tests the appropriateness of the scientific language used by the student.
In all cases, the student is evaluated based on: autonomy of judgment (i.e., whether they have been able to develop critical thinking in evaluating the proposed experiments and methods and their application to different research areas); communication skills in English; the ability to apply the knowledge acquired to problems different from those addressed in class, although within the same field; furthermore, the technical knowledge related to the methods taught will be assessed, as well as the ability to apply the acquired knowledge to solve methodological problems.
Final, intermediate and oral exams can be taken by attending and non-attending students.
Specific procedures for students with disabilities or specific learning disabilities (DSA) will be applied. 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].
The student may take the written exam in two forms: 1. After the end of the course, in the classroom consisting of 10 questions, in two hours. Each module of the course contributes 5 questions. Of these, two are open and require the drafting of a short text. The other 3 questions are closed and require ability to use the data and knowledge acquired to solve problems. 2. Intermediate written exams: one for Genomics (mid way during the course, during the didactic pause) and one for Functional genomics (end of course) [in this order]. The second option is offered only to the students of the current academic year. You need to pass the first one to access the second one. You need to pass both to pass it. Each exam of option 2 consists of 5 questions (open and/or closed), in 90 minutes.
Oral exam: students can take an oral exam for each of the two modules. Oral exam is composed of 5+5 questions (5 for each module) in 30 minutes (for each module). The first question of the Genomics module is the first question is at the student's discretion. Oral exams are upon appointment, independently for each module. The students are evaluated based on their knowledge of the tested topics, their capacity of leading an exposition of a topic for about 5 minutes, their capacity of connecting topics pertaining to different areas of the study subject. Furthermore, the exam tests the appropriateness of the scientific language used by the student.
In all cases, the student is evaluated based on: autonomy of judgment (i.e., whether they have been able to develop critical thinking in evaluating the proposed experiments and methods and their application to different research areas); communication skills in English; the ability to apply the knowledge acquired to problems different from those addressed in class, although within the same field; furthermore, the technical knowledge related to the methods taught will be assessed, as well as the ability to apply the acquired knowledge to solve methodological problems.
Final, intermediate and oral exams can be taken by attending and non-attending students.
Specific procedures for students with disabilities or specific learning disabilities (DSA) will be applied. 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].
AGR/07 - GENETICA AGRARIA - CFU: 5
AGR/12 - PATOLOGIA VEGETALE - CFU: 4
AGR/12 - PATOLOGIA VEGETALE - CFU: 4
Esercitazioni in aula informatica: 40 ore
Esercitazioni: 8 ore
Lezioni: 48 ore
Esercitazioni: 8 ore
Lezioni: 48 ore
Docenti:
Pasquali Matias, Pozzi Carlo Massimo
Turni:
Siti didattici
Docente/i
Ricevimento:
su appuntamento
R056 (via celoria 2)
Ricevimento:
Su appuntamento / upon request
Office - building 21010