Uniwersytet Rolniczy im. Hugona Kołłątaja w Krakowie - Centralny System Uwierzytelniania
Strona główna

Plant and microbial proteomics

Informacje ogólne

Kod przedmiotu: O.1sa.PMB.SM.OOBXY
Kod Erasmus / ISCED: (brak danych) / (brak danych)
Nazwa przedmiotu: Plant and microbial proteomics
Jednostka: Zakład Biochemii
Grupy:
Punkty ECTS i inne: (brak) Podstawowe informacje o zasadach przyporządkowania punktów ECTS:
  • roczny wymiar godzinowy nakładu pracy studenta konieczny do osiągnięcia zakładanych efektów uczenia się dla danego etapu studiów wynosi 1500-1800 h, co odpowiada 60 ECTS;
  • tygodniowy wymiar godzinowy nakładu pracy studenta wynosi 45 h;
  • 1 punkt ECTS odpowiada 25-30 godzinom pracy studenta potrzebnej do osiągnięcia zakładanych efektów uczenia się;
  • tygodniowy nakład pracy studenta konieczny do osiągnięcia zakładanych efektów uczenia się pozwala uzyskać 1,5 ECTS;
  • nakład pracy potrzebny do zaliczenia przedmiotu, któremu przypisano 3 ECTS, stanowi 10% semestralnego obciążenia studenta.

zobacz reguły punktacji
Język prowadzenia: angielski
Skrócony opis:

The course introduces proteomics as a research approach combining basic scientific studies and practical use of variant laboratory techniques which together contribute to contemporary views on modern biology, genetics, biochemistry and environmental sciences. As a large-scale, systemic analysis of proteins, proteomics brings much novel information that broadens the knowledge and current understanding of gene function in the post-genomic era. Proteomics is defined and discussed as expression and functional proteomics as well as bioinformatics, protein mapping and profiling. Basic tools are presented: 2 D electrophoresis, other electrophoretic methods, mass spectrometry, protein fractionation and isolation techniques, spectroscopic methods for studying protein structure and function. Examples of proteome analyses in plant and microbial biotechnology are presented together with the discussion of achievements of proteomic research in terms of general science and application practice.

Pełny opis:

Lectures:

Basic definitions: genome and genomics as contrasted with proteome and proteomics. Proteomics as a compilation of basic and application research; strategies for studying plant and microbial cell protein phenotypes.

Protein life cycle and regulatory mechanisms of protein expression; Expression vs. functional proteomics. Basic stages of proteome analysis; comparison of proteomes of different organisms – plants as well as pro- and eukaryotic microorganisms.

Tools of proteomics: electrophoretic methods including 2DE; data acquisition and visualization, elaboration of 2D-protein maps, construction of databases. Mass spectrometry (MS) – theoretical background and practical performance; applicability for proteome analyses. High-throughput proteomic analyses – automatation, robotization, and application of bioinformatics to elaborate and use internet databases. Basic methods for protein isolation, fractionation and characterization (tissue homogenization, ultracentrifugation, ultrafiltration, salting out, precipitation; liquid chromatography (LC) techniques. Selected methods to study the structure and properties of proteins (X-ray diffraction, protein structure modeling, spectrometric and spectroscopic techniques).

New trends in proteomics: - development of bioinformatics, novel protein identification techniques: recognition chips, protein arrays, lab-on-a-chip; nanomethods for ultrasensitive protein detection.

Examples of proteome analysis in plant science and microbiology.

Laboratory practicals:

Elements of functional proteomics – analysis of inducible enzymes under environmental stress: detection of methanol utilization pathway enzymes of non-conventional methylotrophic yeasts.

1. Yeast cell culture: inoculum preparation and cultivation in fully automated laboratory-scale fermenter (5h).

2. Optimization of fermenter bioprocess parameters, biomass determination and harvest; obtainment of cell-free protein extracts (homogenization via ultrasonication), protein determination (3h).

3. Fractionation and preliminary purification of methylotrophic pathway enzymes – alcohol oxidase and formaldehyde dehydrogenase; protein FPLC chromatography and identification of enzyme activities in the resultant fractions with specific enzymatic assays (7h).

Literatura:

1. Campbell, A. M., Heyer, L. J. Discovering Genomics, Proteomics, and Bioinformatics. Benjamin Cummings, 2002.

2. Dunn M. J. (Ed.) Proteomics Reviews 2001. John Wiley & Sons, 2001.

3. Liebler, D. C. Introduction to Proteomics: Tools for the New Biology. Humana Press, 2002.

4. Marshak, D.R., Kadonaga J.T., Burgess R.R., Knuth M.W., Breenan Jr. W.A., Lin S.-H. Strategies for protein purification and characterization. A laboratory course manual. Cold Spring Harbor Lab. Press, 1996.

5. Pennington S. Proteomics: From Protein Sequence to Function. Dunn M. J. (Ed.) Springer-Verlag New York, Inc., 2000.

6. Sibirny A.A., Titorenko V.I., Gonchar M.V., Ubiyvovk V.M. , Ksheminskaya G. P., Vitvitskaya O.P.: Genetic control of methanol utilization in yeasts. J. Basic Microbiol. 28: 293- 319, 1988.

7. Westermeier R. Naven T. Proteomics in Practice: A Laboratory Manual of Proteome Analysis. John Wiley & Sons, 2002.

8. Bodzon-Kulakowska A., Bierczynska-Krzysik A., Dylag T., Drabik A., Suder P., Noga M., Jarzebinska J., Silberring J. Methods for samples preparation in proteomic research (2007) Journal of Chromatography B 849: 1-31.

9. Campbell, A. M., Heyer, L. J. Discovering Genomics, Proteomics, and Bioinformatics. Benjamin Cummings, 2002.

10. Rose J.K.C., Bashir S., Giovannoni J.J., Jahn M.M., Saravanan R.S. (2004) Tackling the plant proteome: practical approaches, hurdles and experimental tools. The Plant Journal 39: 715-733.

Efekty uczenia się:

EPB2_W01, EPB2_W02, EPB2_W06, EPB2_W07, EPB2_W09

EPB2_U01, EPB2_U02, EPB2_U03, EPB2_U07, EPB2_U11

EPB2_K01, EPB2_K02, EPB2_K05, EPB2_K06

Metody i kryteria oceniania:

test 703

lab class: report 711

Przedmiot nie jest oferowany w żadnym z aktualnych cykli dydaktycznych.
Opisy przedmiotów w USOS i USOSweb są chronione prawem autorskim.
Właścicielem praw autorskich jest Uniwersytet Rolniczy im. Hugona Kołłątaja w Krakowie.
kontakt deklaracja dostępności USOSweb 7.0.3.0 (2024-03-22)