Master's degree in Agri-Food Biotechnology

Master's degree in Agri-Food Biotechnology

Omics sciences - MODULO II (2018/2019)

Course code
4S003719
Credits
6
Coordinator
Alessandra Maria Bossi
Academic sector
CHIM/01 - ANALYTICAL CHEMISTRY
Language of instruction
Italian

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Teaching is organised as follows:
Activity Credits Period Academic staff
Metabolomica laboratorio 2 II semestre Flavia Guzzo
Proteomica laboratorio 1 II semestre Alessandra Maria Bossi
Proteomica teoria 3 II semestre Alessandra Maria Bossi

Go to lesson schedule

Learning outcomes

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MM: Metabolomica laboratorio
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-Plan an experimental design; -interpret some mass spectra; -identify some simple metabolites through the fragmentation trees; -process a complex metabolomics experiment through specific software; -analyse a complex metabolomics experiment using the suitable statistic approaches; -acquire an appropriate language.
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MM: Proteomica laboratorio
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The practicals are intended to furnish wet-lab abilities to the student. It aims at bringing the student closer to the methods and protocols typical of the proteomic research, helping to translate the theory into experimental phases. The bases of the wet-lab proteomic analysis are provided, addressing the issue of the experimental design, the sample processing, the gel separation methods and the silico analysis. The laboratory is aimed at developing experimental proteomics skills. The type of samples selected for the laboratory will be the traceability of the food product.
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MM: Proteomica teoria
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The aim of the module is to provide the theoretical basis for addressing a proteomic analysis. The module begins by providing knowledge about the physico-chemical characteristics of the protein sample and about the related methods to handle and fractionate such sample. Subsequently the proteomics methods are explained, providing knowledge on the separative methods used in proteomics (in gel, gel free), in mass spectrometric analysis of peptides and finally on the identification of proteins. The module aims to provide theoretical-strategic proteomics skills: the knowledge of the protein material and of the sample in analysis, mastering the methods to extract proteins from the sample, decision-making skills in the choice of the separative method; basic analysis skills in mass spectrometry and spectra reading; research skills on in silico databases for protein identification, result validation skills; ability to define a quantitative strategy of proteomic analysis. The educational path aims to provide all the necessary knowledge to mature the ability to apply the proteomics investigation to agro-industrial problems, including the adulteration of foods, the origin and traceability of raw materials.

Syllabus

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MM: Metabolomica laboratorio
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-Simulation of a “real world” experimental design of a metabolomics and transcriptomics experiment: 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 and 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.
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MM: Proteomica laboratorio
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Sample preparation. Separation by means of Gel-Based Proteomics. Proteins and peptides mass spettrometry and mass/mass spectrometry. Protein identification methods and Protein Database Search.
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MM: Proteomica teoria
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The preliminary requisite to study proteomics, is to possess basic concepts of biochemistry and of the principal methods utilized in biochemistry. 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.

Assessment methods and criteria

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MM: Metabolomica laboratorio
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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.
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MM: Proteomica laboratorio
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The exam is aimed at verifying the acquisition by the student of the skills described in the objectives (knowledge of the protein material and of the sample under analysis, mastery of the methods to extract proteins from the sample, decision-making skills in the choice of the separative method; analysis in mass spectrometry and spectra reading, in-silico database research skills for protein identification, result validation skills, ability to define a quantitative strategy of proteomic analysis). The exam is written, open questions, 2 hours. The written exam is integrated, upon student’s request, with an oral verification. The exam will be evaluated on the basis of the student's ability to answer the questions correlating concepts and methods in an appropriate manner and, where proposed, detailing the meaning of equations, or reporting relevant graphs.
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MM: Proteomica teoria
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The exam is aimed at verifying the acquisition by the student of the skills described in the objectives (knowledge of the protein material and of the sample under analysis, mastery of the methods to extract proteins from the sample, decision-making skills in the choice of the separative method; analysis in mass spectrometry and spectra reading, in-silico database research skills for protein identification, result validation skills, ability to define a quantitative strategy of proteomic analysis). The exam is written, open questions, 2 hours. The written exam is integrated, upon student’s request, with an oral verification. The exam will be evaluated on the basis of the student's ability to answer the questions correlating concepts and methods in an appropriate manner and, where proposed, detailing the meaning of equations, or reporting relevant graphs.

Reference books
Activity Author Title Publisher Year ISBN Note
Proteomica laboratorio Ciborowski P. and Silberring J. Proteomic profiling and analytical chemistry: the crossroads. Elsevier 2013 978-0-444-59378-8
Proteomica teoria Ciborowski P. and Silberring J. Proteomic profiling and analytical chemistry: the crossroads. Elsevier 2013 978-0-444-59378-8

STUDENT MODULE EVALUATION - 2017/2018






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