Omics sciences (2017/2018)

Course code
4S003719
Credits
12
Coordinator
Alessandra Maria Bossi
Teaching is organised as follows:
Unit Credits Academic sector Period Academic staff
MODULO II 6 CHIM/01-ANALYTICAL CHEMISTRY See the unit page See the unit page
MODULO I 6 AGR/07-AGRICULTURAL GENETICS See the unit page See the unit page

Learning outcomes

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MM: MODULO II
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------------------------ MM: Metabolomica laboratorio ------------------------ The student will learn the complexity of the various steps of a metabolomics experiment, from the experimental design to the preparation and analysis of the samples (“wet lab”), up to the process and analysis of the data (“dry lab”), through the realization of a “a real world” metabolomics experiment. ------------------------ MM: Proteomica laboratorio ------------------------ To furnish practical knowledge on how to perform a proteomic analysis. ------------------------ MM: Proteomica teoria ------------------------ To furnish the theoretical basis on how to perform a proteomic analysis.
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MM: MODULO I
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------------------------ MM: Metabolomica teoria ------------------------ The main objective of the course is to introduce the metabolomics analysis as an instrument to investigate the biological complexity of cells/tissues/organs/organisms from the point of view of the small molecules, that are the intermediate and end products of the metabolism. The metabolomics approach will be described as pipeline, a chain of connected steps from the experiment design up to the analysis and the data modeling. ------------------------ MM: Trascrittomica laboratorio ------------------------ ------------------------ MM: Trascrittomica teoria ------------------------

Syllabus

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MM: MODULO II
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------------------------ MM: Metabolomica laboratorio ------------------------ -Simulation of a “real world” experimental design of a metabolomics and transcriptomics experiments: the students, organized in work group, will receive an experimental problem and virtual resources (biological resources, department facilities, lab instrumentation and budget), and will be required to lay down an experimental plan. -Extraction of plant medium an low polar metabolites, cleaning of samples through Solid Phase Extraction, visit to the LC-MS facilities. -LC-MS-based -untargeted metabolomics: recognition of molecular ions in LC-MS chromatogram; fragmentation trees; metabolite identification through m/z values and fragmentation trees; -chromatogram processing and Feature Quantification Matrix building; -multivariate and univariate data analysis. ------------------------ MM: Proteomica laboratorio ------------------------ 1. Introduction. 2. Sample preparation. 3. Gel-Based Proteomics. 4. Gel-Free Proteomics. 5. Saple pre-fractionations and analysis of low abundant proteins. 6. Proteins and peptides mass spettrometry and mass/mass spectrometry. 7. Protein identification methods and Protein Database Search. 8. Quantitative Proteomics. 9. Examples of proteomics applied to food. ------------------------ MM: Proteomica teoria ------------------------ 1. Introduction. 2. Sample preparation. 3. Gel-Based Proteomics. 4. Gel-Free Proteomics. 5. Saple pre-fractionations and analysis of low abundant proteins. 6. Proteins and peptides mass spettrometry and mass/mass spectrometry. 7. Protein identification methods and Protein Database Search. 8. Quantitative Proteomics. 9. Examples of proteomics applied to food.
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MM: MODULO I
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------------------------ MM: Metabolomica teoria ------------------------ -the experimental design; -metabolite extraction and preparation for LC-MS; -data formats and conversion; -chromatogram analysis and metabolite annotation; -data preprocessing; the effect of the technique of data normalization; -data processing (with MZmine): m/z feature extraction, chromatogram deconvolution and alignement; production of the Feature Quantification Matrix; -data analysis through multivariate analysis (PCA, PLS-DA, OPLS-DA) and univariate analysis. ------------------------ MM: Trascrittomica laboratorio ------------------------ ------------------------ MM: Trascrittomica teoria ------------------------

Assessment methods and criteria

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MM: MODULO II
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------------------------ MM: Metabolomica laboratorio ------------------------ After a public presentation and a critical discussion of the work of each groups, each student will have a score (from 0 to 2) that will additively contribute to the final partial score of the metabolomics examination ------------------------ MM: Proteomica laboratorio e teoria: open questions related to the theoretical aspects of proteomic analysis and technical aspects of the practicals. Written 2 hours. -
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MM: MODULO I
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------------------------ MM: Metabolomica teoria ------------------------ The examination will be an oral test aimed to verify : -the overall degree of knowledge of the subject of this course; -the scientific language skills. ------------------------ MM: Trascrittomica laboratorio ------------------------ ------------------------ MM: Trascrittomica teoria ------------------------