Omics
A.Y. 2024/2025
Learning objectives
The "Introduction to genomics" module presents to the students the main concepts dealing with genome organization. In facts a graded student in Veterinary Biotechnologies must have basic knowledges on the dimension and architecture of genome and chromosomes, in addition to the meaning of linkage and linkage disequilibrium between loci. Practical applications for animal breeding and veterinary medicine are also presented with the connected doctrinal and statistical tools, for example the use of bead DNA chip for genomic evaluation in cattle, parental exclusion or for general concepts and application in population genomics (F-statistics).
The Proteomic module presents essential information to study the complete proteome of a cell or tissue, its qualitatively and quantitative characterization and the analysis of possible modifications induced by a stimulus. Many different applications of this approach will be illustrated starting from published data.
The Proteomic module presents essential information to study the complete proteome of a cell or tissue, its qualitatively and quantitative characterization and the analysis of possible modifications induced by a stimulus. Many different applications of this approach will be illustrated starting from published data.
Expected learning outcomes
Regarding the genomics module, at the end of the course the student will know the genome size, its organization in chromosomes, the meaning of linkage and Linkage Disequilibrium, the use of DNA bead chips for genomic evaluation in cattle or for ascertaining paternity as well as concepts of population genomics (F statistics).
As far as proteomics is concerned, the student will know the principles and applications of the main proteomic methodologies including; two-dimensional electrophoresis, mass spectrometry, MS and MS/MS, quantitative mass spectrometry, amino-terminal sequence, amino acid analysis and study of complexes. About the ability to do: he will be able to make and interpret a MALDI spectrum , an amino-terminal sequence and a 2D aleltrophoresis. He will also be able to read and discuss specific articles on proteomics
As far as proteomics is concerned, the student will know the principles and applications of the main proteomic methodologies including; two-dimensional electrophoresis, mass spectrometry, MS and MS/MS, quantitative mass spectrometry, amino-terminal sequence, amino acid analysis and study of complexes. About the ability to do: he will be able to make and interpret a MALDI spectrum , an amino-terminal sequence and a 2D aleltrophoresis. He will also be able to read and discuss specific articles on proteomics
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
Analytical and preparative electrophoresis on immobilized pH gradients
Staining methods
Protein maps and sequence analysis of separated proteins on gel
Sequence of proteins and peptides in solution
Amino acid analysis of proteins and peptides
Mass spectrometry in proteomics
Quantitative analysis by mass spectrometry
Studies of post-translational modifications by mass spectrometry
Characterization of protein complexes
Comparative proteomics
Identification of biomarkers and antigens, food control
Applications of omics for environmental sustainability
Statistical processing and bioinformatic analysis of OMICS data. Big data handling
Practical exercises
2D electrophoresis
MALDI mass spectrometry
amino terminal sequence
Use of databases and bioinformatic analyses
Journal Club and discussion of scientific articles
INTRODUCTION TO GENOMICS
1. Genome structure and size, differences between genomes, mutations, SNPs, causative mutations, anonymous synonyms, locus and allele, allele frequencies.
2. HWE and statistical test, chi square, homozygosity and heterozygosity, variation of allele frequencies due to genetic drift, binomial distribution.
3. Variation of genotypic frequencies due to the increase of consanguinity, reduction of heterozygosity, meaning and calculation of relatedness and consanguinity.
4. Loss of heterozygosity, within and between populations, genetic distances and statistics F.
5. Use of genomic data to establish paternity and to attribute a product (authenticity).
6. Genotype-phenotype relationship, simple and dominance effects, variance and heritability of traits, effect of gene substitution.
7. Linkage between two loci, linkage disequilibrium, phase, haplotype, recombination frequency, correlation between two loci, the concept of signatures of selection, conserved genomic regions.
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
9. Genomic index, training population, impact on animal populations, generation interval reduction, a look to the future.
Protein identification and analysis
Analytical and preparative electrophoresis on immobilized pH gradients
Staining methods
Protein maps and sequence analysis of separated proteins on gel
Sequence of proteins and peptides in solution
Amino acid analysis of proteins and peptides
Mass spectrometry in proteomics
Quantitative analysis by mass spectrometry
Studies of post-translational modifications by mass spectrometry
Characterization of protein complexes
Comparative proteomics
Identification of biomarkers and antigens, food control
Applications of omics for environmental sustainability
Statistical processing and bioinformatic analysis of OMICS data. Big data handling
Practical exercises
2D electrophoresis
MALDI mass spectrometry
amino terminal sequence
Use of databases and bioinformatic analyses
Journal Club and discussion of scientific articles
INTRODUCTION TO GENOMICS
1. Genome structure and size, differences between genomes, mutations, SNPs, causative mutations, anonymous synonyms, locus and allele, allele frequencies.
2. HWE and statistical test, chi square, homozygosity and heterozygosity, variation of allele frequencies due to genetic drift, binomial distribution.
3. Variation of genotypic frequencies due to the increase of consanguinity, reduction of heterozygosity, meaning and calculation of relatedness and consanguinity.
4. Loss of heterozygosity, within and between populations, genetic distances and statistics F.
5. Use of genomic data to establish paternity and to attribute a product (authenticity).
6. Genotype-phenotype relationship, simple and dominance effects, variance and heritability of traits, effect of gene substitution.
7. Linkage between two loci, linkage disequilibrium, phase, haplotype, recombination frequency, correlation between two loci, the concept of signatures of selection, conserved genomic regions.
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
9. Genomic index, training population, impact on animal populations, generation interval reduction, a look to the future.
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; from the second oral exam session
Genomics: Written with open questions and multiple choice in the first session; 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