Bi6725 Advanced Methods in Cell Biology

Faculty of Science
Autumn 2008
Extent and Intensity
0/2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: graded credit.
Teacher(s)
prof. RNDr. Alois Kozubík, CSc. (seminar tutor)
prof. RNDr. Jiřina Hofmanová, CSc. (seminar tutor)
RNDr. Miroslav Machala, CSc. (seminar tutor)
Mgr. Jiřina Medalová, Ph.D. (seminar tutor)
Mgr. Karel Souček, Ph.D. (seminar tutor)
prof. RNDr. Jan Vondráček, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Alois Kozubík, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Alois Kozubík, CSc.
Prerequisites
The subject follows and belongs to the logical unit of practical courses of Animal Physiology and Special Methods of Animal Physiology.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Innovated course with theoretic and practical parts follows the related subjects to bring the knowledge of mainly bachelor students on more elaborated level. Introduced well-established and optimalized techniques help also students of diploma and Ph.D. thesis to perform their experiments. Students make use of well-equipped facility of Institute of Biophysics of Academy of Sciences of the Czech Republic, v.v.i., to get practically acquainted with up-to-date trends and modern techniques used in basic research of molecules, specific cells and cell populations. The main goals of the course are: Introducing both the classical and modern techniques used in basic and applied research (see Sylabus). Allow students to evolve their laboratory skills. Enlarge the methodic background of students to help them to perform their diploma thesis.
Syllabus
  • 1. Cell cultures
  • Assessment of cell count and viability: laboratory equipment, work in the sterile flow box, sorts of plastic for cell culture, safety rules in molecular biology labs, passaging of cells, counting of cells with use of Coulter Counter, assessment of cells viability by eosin and propidium iodide dye exclusion assays.
  • Detection of apoptotic cells: assessment of apoptotic index - DAPI staining (detection of fluorescent cells with condensed and fragmented chromatin). Measurement of mitochondrial membrane potential of apoptotic cells by TMRE (tetramethyl rhodamin ethylester) by flow cytometry.
  • Detection of differentiation level of leukemic cells: Detection of surface markers of differentiation CD11b and CD14 in myeloid cell line HL-60 by means of flow cytometry and direct immunocytochemistry. Assessment of oxidative burst of monocytic cells stimulated by phagocytosis activators (zymosan, phorbol myristate acetate) by plate luminometer.
  • Detection of differentiation of colon cancer cells (cell line HT-29): assessment of alkaline phosphatase by colorimetry (alkaline phosphatase cleaves colorless substrate 4-p-nitrophenyl phopshate producing yellow color).
  • 2. Fluorescence and confocal microscopy:
  • Principle and function of fluorescence microscope (advantages and limits), differences between conventional and confocal microscopy. Observation of 3D fixed interphase nuclei containing fluorescently labeled gene. Second fluorescent label stains the whole chromosome in which the target gene is localised.
  • 3. Biochemical methods:
  • Preparation of cell lysate for Western blotting and isolation of RNA: Methods of cell lysate preparation - both for western blotting detection of proteins and isolation of RNA. Assessment of protein concentration using Bio-Rad DC kit. Electrophoresis and transfer of proteins to membrane - separation of proteins by SDS-PAGE, semi-dry electroblotting of proteins from gel to PVDF membrane
  • Immunodetection:
  • Immunodetection of beta-actin by indirect immunochemistry (primary unlabelled anti-beta-actin Ab) and secondary antibody conjugated with horseradish peroxidase in samples from previous lecture. Visualisation of immunocomplex by ECL plus kit.
  • Isolation of whole RNA, assessment of its concentration and quality: Isolation of RNA from prepared cell lysate using the commercially available kit, assessment of concentration and purity of RNA using the Nanodrop ND-1000 Spectrophotometer device.
  • ELISA (Enzyme Linked Immunosorbent Assay) technique: Detection of TNF-alpha concentration in medium of differentiated THP-1 myeloid cells by commercially available Duoset kit from R&D system. Cells were treated for 24 hours by different concentrations of endotoxin.
Literature
  • Cell culture and upstream processing. Edited by M. Butler. 1st ed. New York: Taylor & Francis. xiv, 187. ISBN 9780415399692. 2007. info
  • Mammalian cell culture : essential techniques. Edited by A. Doyle - J. B. Griffiths. Chichester: John Wiley & Sons. xv, 173. ISBN 0471970573. 1997. info
  • Cancer cell culture : methods and protocols. Edited by Simon P. Langdon. Totowa, N.J.: Humana Press. xii, 360. ISBN 1588290794. 2004. info
  • Animal cell culture :a practical approach. Edited by R. Ian Freshney. 2nd ed. Oxford: Oxford University Press. xix, 329 s. ISBN 0-19-963213-8. 1992. info
  • Cell biological appplications of confocal microscopy. Edited by Brian Matsumoto. 2nd ed. Amsterdam: Academic Press. xii, 507. ISBN 0125804458. 2002. info
  • Molecular cloning, A laboratory manual, Vol. 1-3, Eds. J. Sambrook and D. W. Russell, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 2001
  • Short protocols in molecular biology, Vol. 1 and 2, 5th edition, John Wiley and Sons, Inc., 2002
  • Current protocols in cytometry, Vol. 1 and 2, Ed. J. P. Robinson, John Wiley and Sons, Inc., 1997
  • Methods in Cell Biology, Vol. 75, Cytometry, 4th edition, New developments, Eds. Z. Darzynkiewicz, M. Roederer, H. J. Tanke, Elsevier Academic Press, 2004
  • CROWTHER, John R. The ELISA guidebook. Totowa, N.J.: Humana Press. xi, 421. ISBN 0896037282. 2001. info
Assessment methods
Short theoretic lectures followed by practical course; homeworks, class discussion with skilled teacher. Credit requirements: Individual evaluation of results and answering questions in protocols, final written test.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2010 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Autumn 2006, Autumn 2007, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017.
  • Enrolment Statistics (Autumn 2008, recent)
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