Omics
A.Y. 2025/2026
Learning objectives
The aim of the OMICS course is for students to develop knowledge and understanding of genomics and advanced proteomic approaches applied to the qualitative and quantitative study of proteins and peptides in cells and tissues of various origins. Specifically, the Introduction to Genomics module introduces students to the key concepts underlying genome organization. The Proteomics module provides essential information on the main techniques for studying the entire proteome of a cell or tissue, for its qualitative and quantitative characterization, and for analyzing possible changes in response to a stimulus. The broad range of potential applications of this approach will be illustrated, starting with a discussion of published experimental data.
Expected learning outcomes
1. Knowledge and Understanding: Regarding the Introduction to Genomics module, by the end of the course, students will demonstrate knowledge of genome size, its organization into chromosomes, the meaning of linkage and linkage disequilibrium, as well as concepts of population genomics (F-statistics).
Regarding the Proteomics module, students will demonstrate knowledge of the principles and applications of the main proteomic methodologies, including: two-dimensional electrophoresis, mass spectrometry, first- and second-order mass analysis, quantitative mass spectrometry, amino-terminal sequencing, amino acid analysis, and the study of complexes.
2. Ability to Apply Knowledge and Understanding: Regarding the Introduction to Genomics module, students will demonstrate knowledge and concepts useful for the use of DNA bead chips for genomic evaluation in cattle or for paternity determination. In the Proteomics module, students must demonstrate the ability to perform and/or interpret a MALDI and ESI mass spectrum, an amino-terminal sequence, and 2D electrophoresis. They must also be able to read and discuss scientific articles related to proteomics and omics applications.
3. Critical thinking and judgment skills: Students must demonstrate the ability to critically argue the information they have learned. This is addressed in the Introduction to Genomics module through specific lessons on case studies and group work. In the Proteomics module, group journal clubs are organized with presentations prepared by students.
4. Ability to communicate what they have learned: Students must demonstrate the ability to express themselves with scientifically appropriate terminology, particularly regarding terminology related to genomics and proteomics. Exercises and group work are intended to foster the ability to express themselves correctly and the ability to engage in scientific discussion with peers.
5. Ability to continue studying independently throughout one's life: the student must demonstrate the ability to use the knowledge acquired to interpret data and develop new experimental projects, drawing on available sources of knowledge and good mental organization.
Regarding the Proteomics module, students will demonstrate knowledge of the principles and applications of the main proteomic methodologies, including: two-dimensional electrophoresis, mass spectrometry, first- and second-order mass analysis, quantitative mass spectrometry, amino-terminal sequencing, amino acid analysis, and the study of complexes.
2. Ability to Apply Knowledge and Understanding: Regarding the Introduction to Genomics module, students will demonstrate knowledge and concepts useful for the use of DNA bead chips for genomic evaluation in cattle or for paternity determination. In the Proteomics module, students must demonstrate the ability to perform and/or interpret a MALDI and ESI mass spectrum, an amino-terminal sequence, and 2D electrophoresis. They must also be able to read and discuss scientific articles related to proteomics and omics applications.
3. Critical thinking and judgment skills: Students must demonstrate the ability to critically argue the information they have learned. This is addressed in the Introduction to Genomics module through specific lessons on case studies and group work. In the Proteomics module, group journal clubs are organized with presentations prepared by students.
4. Ability to communicate what they have learned: Students must demonstrate the ability to express themselves with scientifically appropriate terminology, particularly regarding terminology related to genomics and proteomics. Exercises and group work are intended to foster the ability to express themselves correctly and the ability to engage in scientific discussion with peers.
5. Ability to continue studying independently throughout one's life: the student must demonstrate the ability to use the knowledge acquired to interpret data and develop new experimental projects, drawing on available sources of knowledge and good mental organization.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
PROTEOMICS
Protein identification and analysis ( 4 hours)
Analytical and preparative electrophoresis on immobilized pH gradient and staining methods (2 hours)
Protein maps and sequence analysis of separated proteins on gel (2 hours)
Sequence of proteins and peptides in solution (2 hours)
Amino acid analysis of proteins and peptides (2 hours)
Mass spectrometry in proteomics (10 hours)
Quantitative analysis by mass spectrometry (2 hours)
Studies of post-translational modifications by mass spectrometry
Characterization of protein complexes (2 hours)
Comparative proteomics (2 hours)
Identification of biomarkers and antigens, food control (2 hours)
Applications of omics for environmental sustainability (2 hours)
Statistical processing and bioinformatic analysis of OMICS data. Big data handling (2 hours)
Practical exercises
2D electrophoresis (4 hours)
MALDI mass spectrometry (2 hours)
amino terminal sequence (2 hours)
Use of databases and bioinformatic analyses (2 hours)
Journal Club and discussion of scientific articles (2 hours)
INTRODUCTION TO GENOMICS
1. Genome structure and size, differences between genomes, mutations, SNPs, causative mutations, anonymous synonyms, locus and allele, allele frequencies (2h)
2. HWE and statistical test, chi square, homozygosity and heterozygosity, variation of allele frequencies due to genetic drift, binomial distribution (2h).
3. Variation of genotypic frequencies due to the increase of consanguinity, reduction of heterozygosity, meaning and calculation of relatedness and consanguinity (2h).
4. Loss of heterozygosity, within and between populations, genetic distances and statistics F (2h).
5. Use of genomic data to establish paternity and to attribute a product (authenticity) (2h).
6. Genotype-phenotype relationship, simple and dominance effects, variance and heritability of traits, effect of gene substitution (2h).
7. Linkage between two loci, linkage disequilibrium, phase, haplotype, recombination frequency, correlation between two loci, the concept of signatures of selection, conserved genomic regions (2h).
8. Bead-chip, analysis in LD, MD and HD, association between anonymous markers and loci of economic significance, estimation of the gene substitution effect of precise genomic regions, analogy with the infinitesimal model (2h)
9. Genomic index, training population, impact on animal populations, generation interval reduction, a look to the future (2h).
Protein identification and analysis ( 4 hours)
Analytical and preparative electrophoresis on immobilized pH gradient and staining methods (2 hours)
Protein maps and sequence analysis of separated proteins on gel (2 hours)
Sequence of proteins and peptides in solution (2 hours)
Amino acid analysis of proteins and peptides (2 hours)
Mass spectrometry in proteomics (10 hours)
Quantitative analysis by mass spectrometry (2 hours)
Studies of post-translational modifications by mass spectrometry
Characterization of protein complexes (2 hours)
Comparative proteomics (2 hours)
Identification of biomarkers and antigens, food control (2 hours)
Applications of omics for environmental sustainability (2 hours)
Statistical processing and bioinformatic analysis of OMICS data. Big data handling (2 hours)
Practical exercises
2D electrophoresis (4 hours)
MALDI mass spectrometry (2 hours)
amino terminal sequence (2 hours)
Use of databases and bioinformatic analyses (2 hours)
Journal Club and discussion of scientific articles (2 hours)
INTRODUCTION TO GENOMICS
1. Genome structure and size, differences between genomes, mutations, SNPs, causative mutations, anonymous synonyms, locus and allele, allele frequencies (2h)
2. HWE and statistical test, chi square, homozygosity and heterozygosity, variation of allele frequencies due to genetic drift, binomial distribution (2h).
3. Variation of genotypic frequencies due to the increase of consanguinity, reduction of heterozygosity, meaning and calculation of relatedness and consanguinity (2h).
4. Loss of heterozygosity, within and between populations, genetic distances and statistics F (2h).
5. Use of genomic data to establish paternity and to attribute a product (authenticity) (2h).
6. Genotype-phenotype relationship, simple and dominance effects, variance and heritability of traits, effect of gene substitution (2h).
7. Linkage between two loci, linkage disequilibrium, phase, haplotype, recombination frequency, correlation between two loci, the concept of signatures of selection, conserved genomic regions (2h).
8. Bead-chip, analysis in LD, MD and HD, association between anonymous markers and loci of economic significance, estimation of the gene substitution effect of precise genomic regions, analogy with the infinitesimal model (2h)
9. Genomic index, training population, impact on animal populations, generation interval reduction, a look to the future (2h).
Prerequisites for admission
Basic information of Biochemistry and Genomics
Teaching methods
Lectures and laboratory exercises.
Seminars and exercises in English will also be held
Seminars and exercises in English will also be held
Teaching Resources
Notes, seminars and online courses
Didactic material provided and transmitted by the teacher. a set of files on ariel is also available
Recommended texts:
· Introducing Proteomics, from concepts to sample preparation, mass spectrometry and data analysis by J. Lovric (2011), Wiley-Blackwell Publishers
· Introduction to proteomics, Principles and Applications (2010) N. Mishra, John Wiley & Sons, Inc., Publication.
- Proteomica, Alberio, Fasano, Roncada, Edises Editions
-
Didactic material provided and transmitted by the teacher. a set of files on ariel is also available
Recommended texts:
· Introducing Proteomics, from concepts to sample preparation, mass spectrometry and data analysis by J. Lovric (2011), Wiley-Blackwell Publishers
· Introduction to proteomics, Principles and Applications (2010) N. Mishra, John Wiley & Sons, Inc., Publication.
- Proteomica, Alberio, Fasano, Roncada, Edises Editions
-
Assessment methods and Criteria
Proteomics: Written exam with open questions on all the topics covered in the lessons (2 hours)
Genomics: Written with open questions and multiple choice in the first session on all the topics covered in the lessons (1 hours); from the second oral exam session
Genomics: Written with open questions and multiple choice in the first session on all the topics covered in the lessons (1 hours); from the second oral exam session
BIO/10 - BIOCHEMISTRY - University credits: 7
BIO/18 - GENETICS - University credits: 3
BIO/18 - GENETICS - University credits: 3
Practicals: 12 hours
Lessons: 54 hours
Lessons: 54 hours
Professors:
Minozzi Giulietta, Tedeschi Gabriella
Educational website(s)
Professor(s)
Reception:
By appointment via email