Učni načrt predmeta

Predmet:
Proteomika
Course:
Proteomics
Študijski program in stopnja /
Study programme and level		 Študijska smer /
Study field		 Letnik /
Academic year		 Semester /
Semester
Nanoznanosti in nanotehnologije, 3. stopnja Bioznanosti 1 1
Nanosciences and Nanotechnologies, 3rd cycle Biosciences 1 1
Vrsta predmeta / Course type
Izbirni / Elective
Univerzitetna koda predmeta / University course code:
NANO3-828
Predavanja
Lectures		 Seminar
Seminar		 Vaje
Tutorial		 Klinične vaje
work		 Druge oblike
študija		 Samost. delo
Individ. work		 ECTS
15 15 15 105 5

*Navedena porazdelitev ur velja, če je vpisanih vsaj 15 študentov. Drugače se obseg izvedbe kontaktnih ur sorazmerno zmanjša in prenese v samostojno delo. / This distribution of hours is valid if at least 15 students are enrolled. Otherwise the contact hours are linearly reduced and transfered to individual work.

Nosilec predmeta / Course leader:
doc. dr. Robert Vidmar
Sodelavci / Lecturers:
izr. prof. dr. Marko Fonović
Jeziki / Languages:
Predavanja / Lectures:
Slovenščina, angleščina/ Slovenian, English
Vaje / Tutorial:
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Poznavanje osnov biokemije in biokemijskih analitskih metod, pridobljenih na dodiplomskih študijih biokemije, kemije, biologije ali farmacije.

Knowledge of biochemistry and biochemical analytical methodology, acquired in undergraduate courses of biochemistry, chemistry, biology or pharmacy.

Vsebina:
Content (Syllabus outline):

Metode ločevanja proteinov: priprava vzorca, PAGE, 2D-PAGE, DIGE, HPLC, MudPIT, afinitetna kromatografija

Masna spektrometrija: osnove masne spektrometrije, vrste in komponente masnih spektrometrov, MALDI, ESI, CID, ETD, ECD

Kvantitativna proteomika: ICAT, SILAC, iTRAQ, absolutna kvantifikacija

Bioinformatika: statistična obdelava podatkov, proteinske in genomske podatkovne baze, algoritmi za identifikacijo MS/MS spektrov, “de novo” sekveniranje

Proteomika in reševanje bioloških problemov: “top down” in “bottom up” pristop, posttranslacijske modifikacije proteinov, proteinski kompleksi, biomarkerji

Protein separation techniques: sample preparation, PAGE, 2D-PAGE, DIGE, HPLC, MudPIT, affinity chromatography.

Mass spectrometry: basic principles of mass spectrometry, types and components of mass spectrometers, MALDI, ESI, CID, ETD, ECD.

Quantitative proteomics: ICAT, SILAC, iTRAQ, absolute quantification

Bioinformatics: statistical data evaluation, protein and genomic databases, identification of MS/MS spectra, “de novo” sequencing

Proteomics and biology: “top down” and “bottom up” approach, protein posttranslational modifications, protein complexes, biomarkers.

Temeljna literatura in viri / Readings:

Principles of Proteomics (Advanced Text Series) R. M. Twyman, BIOS Scientific Publ, 2013.
Protein analysis by shotgun/bottom-up proteomics.Y. Zhang, B.R. Fonslow, B. Shan, M.C. Baek, J.R. 3rd Yates. Chem Rev. 2013 Apr 10;113(4):2343-94.
Proteomics in Practice: A Guide to Successful Experimental Design, R. Westermeier, T. Naven, H. R. Höpker, Wiley-VCH, 2008.
Computational Methods for Mass Spectrometry Proteomics, I. Eidhammer, K. Flikka, L. Martens, S. O. Mikalsen, Wiley-Interscience, 2008.

Cilji in kompetence:
Objectives and competences:

Splošne kompetence:
- obvladanje raziskovalnih metod in postopkov, razvoj kritične in samokritične presoje,
- sposobnost uporabe znanja v praksi,
- razvoj komunikacijskih sposobnosti in spretnosti, posebej komunikacije v mednarodnem okolju,
- kooperativnost, delo v skupini (in v mednarodnem okolju).

Predmetnospecifične kompetence:
Študent se bo seznanil s teoretičnimi osnovami proteomike in z njeno uporabo v biomedicinskih raziskavah. Pri svojem delu bo uporabljal najnovejšo tujo strokovno literaturo, kar bo izboljšalo njegove sposobnosti uporabe tujega jezika in kritičnega pogleda na objavljeno raziskovalno delo.

General Competences:
- the student will master research methods and procedures and develop skills for critical assessment of his activities,
- the student will be able to put his knowledge into practice,
- the student will develop communications skills to present research achievement in the international environment,
- training for team work (in international environment)

Course Specific Competences:
Student will learn theoretical background of proteomics and its application in biomedical research. During his study he will use the newest scientific literature, which will improve his foreign language skills and his ability to critically view the published research.

Predvideni študijski rezultati:
Intendeded learning outcomes:

Osvojitev osnovnih principov proteomike in z njo povezane instrumentacije, kamor sodi poznavanje tehnik priprave vzorca, metod za separacijo proteinov in razumevanje delovanja masnih spektrometrov. Razumevanje osnovnih programskih orodij in algoritmov za statistično obdelavo masno spektroskopskih podatkov in njihovo uporabo za iskanje po proteinskih in genomskih bazah podatkov. Pregled nad različnimi pristopi k reševanju biomedicinskih raziskovalnih problemov s pomočjo proteomike.

Understanding of the basic principles of proteomics, such as sample preparation, protein separation and general knowledge of mass spectrometry instrumentation. Understanding of the software tools for statistical evaluation of mass spectrometry data and its application in protein and genomic database searches. Overview of proteomic approaches toward solving of various biomedical scientific problems.

Metode poučevanja in učenja:
Learning and teaching methods:

Predavanja/konzultacije in seminar.

Lectures/consultations and seminar work.

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Seminar
50 %
Seminar
Ustni izpit
50 %
Oral exam
Reference nosilca / Lecturer's references:
1. TUŠAR, Livija, LOBODA, Jure, VIDMAR, Robert, VIZOVIŠEK, Matej, MIHELIČ, Marko, FONOVIĆ, Marko, HORVAT, Jaka, KOSEC, Gregor, TURK, Boris, TURK, Dušan, et al. Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Communications biology. 2023, vol. 6, str. 450-1-450-15. ISSN 2399-3642. DOI: 10.1038/s42003-023-04772-8
2. RAZPOTNIK, Rok, VIDMAR, Robert, FONOVIĆ, Marko, ROZMAN, Damjana, REŽEN, Tadeja (avtor, korespondenčni avtor). Circular RNA hsa_circ_0062682 binds to YBX1 and promotes oncogenesis in hepatocellular carcinoma. Cancers. Sep. 2022, vol. 14, no. 18, str. 1-25. ISSN 2072-6694
3. ANDRÁS SCHVARCZ, Csaba, FONOVIĆ, Marko, VIDMAR, Robert, et al. Modulated electro-hyperthermia induces a prominent local stress response and growth inhibition in mouse breast cancer isografts. Cancers. 2021, vol. 13, no. 7, str. 1744-1-1744-24. ISSN 2072-6694. DOI: 10.3390/cancers13071744
4. BERNEGGER, Sabine, VIDMAR, Robert, FONOVIĆ, Marko, POSSELT, Gernot, TURK, Boris, WESSLER, Silja. Identification of Desmoglein-2 as a novel target of Helicobacter pylori HtrA in epithelial cells. Cell communication and signaling. 2021, vol. 19, no. 1, str. 108-1-108-12. ISSN 1478-811X. DOI: 10.1186/s12964-021-00788-x
5. RÓKA, Beáta, TOD, Pál, KAUCSÁR, Tamás, VIZOVIŠEK, Matej, VIDMAR, Robert, TURK, Boris, FONOVIĆ, Marko, SZÉNÁSI, Gábor, HAMAR, Péter. The acute phase response is a prominent renal proteome change in sepsis in mice. International journal of molecular sciences. 2020, vol. 21, no. 1, str. 200-1-200-20. ISSN 1661-6596. DOI: 10.3390/ijms21010200