ANALYTICAL AND CLINICAL PROTEOMICS (2013/2014)

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Course code
4S000680
Credits
6
Coordinator
Daniela Cecconi
Other available courses
Other available courses
    Academic sector
    CHIM/01 - ANALYTICAL CHEMISTRY
    Language of instruction
    Italian
    Teaching is organised as follows:
    Activity Credits Period Academic staff Timetable
    teoria 5 II semestre Daniela Cecconi
    esercitazioni 1 II semestre Daniela Cecconi

    Lesson timetable

    II semestre
    Activity Day Time Type Place Note
    teoria Tuesday 8:30 AM - 10:30 AM lesson Lecture Hall H  
    teoria Thursday 11:30 AM - 1:30 PM lesson Lecture Hall H  

    Learning outcomes

    Proteomics is the large-scale study of proteins. It is an emerging scientific research which can be applied for example to food (to find allergen for example) and plants research (for example to study plant pathogen response), as well as to biomedical research (clinical proteomics).
    In particular, clinical proteomics is the science that aims to develop technologies for the treatment of patients through the analysis of proteomes of healthy and sick cells. This research area aimed to identify proteins that can be used as early markers in blood, urine, or tissues of cancer patients, or that may predict response to therapy or the relapse after treatment.

    Syllabus

    PROTEOMICS

    Analytical proteomics (LM9+LM7):

    1. Introduction.

    2. Sample preparation.

    3. Gel-based separation.

    4. 2D gel Image analysis.

    5. Gel-free separation.

    6. Pre-fractionation of low abundance proteins.

    7. Analysis of proteins/peptides by Mass Spectrometry.

    8. Analysis of proteins/peptides by Tandem Mass Spectrometry.

    9. Analysis of mass spectra and database search for protein identification.

    10. Differential and Quantitative proteomics.

    11. Characterization of post-translational modifications.

    12. Proteomics in agro-food and biomedical areas.


    Clinical proteomics (LM9):

    13. Application of Proteomics in Cancer Research.

    14. Mantle cell lymphoma: resveratrol treatment, and phosphoproteomic analysis.

    15. Pancreatic cancer: phosphoproteomic profiling of cells treated with CB1 or CB2 agonists; and shotgun analysis of stem cells.

    16. From iron-diseases to hypertension: application of clinical proteomics.

    17. Macrophages and iron metabolism, splenic lymphoma SMZL

    18. Intrauterine Growth Retardation and Cardiovascular Diseases.

    19. Autoimmune disease.

    20. Bacterial and viral infections.




    Laboratory (1 CFU)

    Day 1:
    Rehydration of 7 cm IPG with protein extract
    Preparation of buffers and solutions for 2-DE analysis
    Polymerization of 12% T gel
    Isoelectrofocusing by using PROTEAN® IEF Cell (Bio-Rad)


    Day 2:
    IPG strip equilibration
    Interfacing with the second dimension
    Second dimension by Mini-PROTEAN® 3 Dodeca™ Cell (Bio-Rad)
    Staining of 2-DE maps with Coomassie and/or SyproRuby

    Day 3:
    Destaining and acquisition of images by VersaDoc™ MP 1000 system (Bio-Rad)
    Image analysis by PDQuest software (Bio-Rad) (classroom gamma)
    Analysis of mass spectra and database searching with Mascot

    Assessment methods and criteria

    Labs activities are mandatory.

    LM7: written
    LM9: written + paper presentation

    Recommended text:
    “Introducing Proteomics: From concepts to sample separation, mass spectrometry and data analysis” Josip Lovric, Wiley-Blackwell