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Chapter 6. In Vitro Techniques

  1. J. Robin Harris47,
  2. John Graham48,
  3. David Rickwood49
  1. J. Robin Harris47,
  2. Geneviève Almouzni1,
  3. Doris Kirschner2,
  4. Daniela Dimitrova3,
  5. Jeffrey A. Nickerson4,
  6. Jean Underwood5,
  7. Stefan Wagner5,
  8. Barbara Korbei6,
  9. Roland Foisner6,
  10. Tobias C. Walther7,
  11. Martin Hetzer8,
  12. Reiner Peters9,
  13. Ivan Walev10,
  14. Anton I. P. M. de Kroon11,
  15. Rutger W. H. M. Staffhorst11,
  16. Ben de Kruijff11,
  17. Koert N. J. Burger12,
  18. Luis Eduardo Soares Netto13,
  19. Eric Bertrand14,
  20. Judie B. Alimonti15,
  21. Arnold H. Greenberg16,†,
  22. Jinnan Xiao17,
  23. Anuradha Pradhan17,
  24. Yuechueng Liu17,
  25. Jacques Paiement18,
  26. Robin Young18,
  27. Félix M. Goñi19,
  28. Ana-Victoria Villar19,
  29. F.-Xabier Contreras19,
  30. Alicia Alonso19,
  31. Brian J. Peter20,
  32. Ian G. Mills21,
  33. Matthew K. Higgins22,
  34. William J. Brown23,
  35. K. Chambers23,
  36. A. Doody23,
  37. C. Yan Cheng24,
  38. Dolores D. Mruk24,
  39. Chunhong Yang25,
  40. Helmut Kirchhoff26,
  41. Winfried Haase,
  42. Stephanie Boggasch25,
  43. Harald Paulsen25,
  44. Julie Benesova27,
  45. Sven-T. Liffers27,
  46. Matthias Rögner27,
  47. Ya-sheng Gao28,
  48. Elizabeth Sztul29,
  49. Meinolf Thiemann30,
  50. H. Dariush Fahimi31,
  51. Robert Gniadecki32,
  52. Barbara Gajkowska33,
  53. Susan L. Bane34,
  54. John F. Hess35,
  55. John C. Voss36,
  56. Paul G. Fitzgerald35,
  57. Shin-ichi Hisanaga37,
  58. Takahiro Sasaki38,
  59. Kenji Uéda38,
  60. Terrence Town39,
  61. Jun Tan40,
  62. Nathaniel G. N. Milton41,
  63. Richard Chi42,
  64. Thomas C. S. Keller III42,
  65. Marina Kriajevska43,
  66. Igor Bronstein44,
  67. Eugene Lukanidin45,
  68. David F. Holmes46,
  69. Karl E. Kadler46

Published Online: 3 JUL 2006

DOI: 10.1002/0470033487.ch6

Book Title

Cell Biology Protocols

Cell Biology Protocols

Additional Information

How to Cite

Harris, J. R., Almouzni, G., Kirschner, D., Dimitrova, D., Nickerson, J. A., Underwood, J., Wagner, S., Korbei, B., Foisner, R., Walther, T. C., Hetzer, M., Peters, R., Walev, I., de Kroon, A. I. P. M., Staffhorst, R. W. H. M., de Kruijff, B., Burger, K. N. J., Netto, L. E. S., Bertrand, E., Alimonti, J. B., Greenberg, A. H., Xiao, J., Pradhan, A., Liu, Y., Paiement, J., Young, R., Goñi, F. M., Villar, A.-V., Contreras, F.-X., Alonso, A., Peter, B. J., Mills, I. G., Higgins, M. K., Brown, W. J., Chambers, K., Doody, A., Cheng, C. Y., Mruk, D. D., Yang, C., Kirchhoff, H., Haase, W., Boggasch, S., Paulsen, H., Benesova, J., Liffers, S.-T., Rögner, M., Gao, Y.-s., Sztul, E., Thiemann, M., Fahimi, H. D., Gniadecki, R., Gajkowska, B., Bane, S. L., Hess, J. F., Voss, J. C., Fitzgerald, P. G., Hisanaga, S.-i., Sasaki, T., Uéda, K., Town, T., Tan, J., Milton, N. G. N., Chi, R., Keller, T. C. S., Kriajevska, M., Bronstein, I., Lukanidin, E., Holmes, D. F. and Kadler, K. E. (2006) In Vitro Techniques, in Cell Biology Protocols (eds J. R. Harris, J. Graham and D. Rickwood), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/0470033487.ch6

Editor Information

  1. 47

    Institute of Zoology, Johannes Gutenberg-Universität, University of Mainz, D-55099 Mainz, Germany

  2. 48

    JG Research Consultancy, 34 Meadway, Upton Wirral CH49 6IQ, UK

  3. 49

    Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK

Author Information

  1. 1

    Institut Curie, CNRS, UMR 218, Section Recherche, 26 rue Ulm, F-75248 Paris 05, France

  2. 2

    Institut Carie, 26 rue d'Ulm, 75248 Paris Cedex 05, France

  3. 3

    Center for Single Molecule Biophysics and Department of Microbiology, 304 Sherman Hall, SUNY at Buffalo, Buffalo, NY 14214, USA

  4. 4

    Department of Cell Biology, School of Medicine, University of Massachusetts, 55 Lake Avenue N., Worcester, MA 01655, USA

  5. 5

    Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Avenue, Worcester, MA 01655, USA

  6. 6

    Department of Molecular Cell Biology, Institute of Medical Biochemistry, Vienna Biocenter, University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria

  7. 7

    EMBL, Gene Expression Programme, Meyerhofstrasse 1, 69117 Heidelberg, Germany

  8. 8

    Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA

  9. 9

    Institut für Medizinische Physik und Biophysik, Universität Münster, Robert-Koch-Straß 31, D-48149 Münster, Germany

  10. 10

    Institute for Medical Microbiology and Hygiene, University of Mainz, Hochhaus Augustusplatz, D-55131 Mainz, Germany

  11. 11

    Department Biochemistry of Membranes, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Padualaan 8, 3584 CH Utrecht, The Netherlands

  12. 12

    Department of Biochemical Physiology, Institute of Biomembranes, Room W210, Padualaan 8, 3584 CH Utrecht, The Netherlands

  13. 13

    Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277; Sala 327, Cidade Universitária, CEP 05508-900, São Paulo-SP, Brazil

  14. 14

    Novartis Pharma AG, CH-4002, Switzerland

  15. 15

    Special Pathogens Program, National Microbiology Laboratory, H2380, 1015 Arlington Ave. Winnipeg, Manitoba, R3E 3R2, Canada

  16. 16

    University of Manitoba, Department of Medical Microbiology, 539-730 William Avenue, Winnipeg, MB, R3E OV9, Canada

  17. 17

    Department of Pathology, University of Oklahoma Health Services Center, Oklahoma City, OK 73104, USA

  18. 18

    Département de Pathologie et Biologie Cellulaire, Université de Montréal N-813, Pavilion Principal, 2900 Edouard-Montpetit, Montréal, Québec H3T 1J4, Canada

  19. 19

    Universidad del País Vasco, EHU, CSIC, Unidad Biofis, Aptdo 644, E-48080, Spain

  20. 20

    McMahon Laboratory, Neurobiology Division, MRC-LMB, Hills Road, Cambridge CB2 2QH, UK

  21. 21

    Dept. of Neurobiology, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK

  22. 22

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK

  23. 23

    Biochemistry, Molecular and Cell Biology Sections, Cornell University, Ithaca, NY 14853, USA

  24. 24

    Population Council, Center of Biomedical Research, 1230 York Avenue, New York NY 10021, USA

  25. 25

    Institut für Allgemeine Botanik der Johannes-Gutenberg-Universität, Müllerweg 6, D-55099 Mainz, Germany

  26. 26

    Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossplatz 2, D-48149 Münster, Germany

  27. 27

    Lehrstuhl für Biochemie der Pflanzen, Ruhr-Universität Bochum, D-447780 Bochum, Germany

  28. 28

    Department of Pathology, Duke University Medical Center, Box No. 3020, Rm 225, Jones Bldg, Durham, NC 27, USA

  29. 29

    Department of Cell Biology, University of Alabama, McCullum Bldg, Rm 668, 1530 S. 3rd Avenue, Birmingham, AL 35294, USA

  30. 30

    Graffinity Pharmaceuticals AG, Im Neuenheimer Feld 518-519, D-69120 Heidelberg, Germany

  31. 31

    Institute of Anatomy and Cell Biology, University of Heidelberg, INF 307, Neuenheimer Feld 307, D-69120 Heidelberg, Germany

  32. 32

    University of Copenhagen, Bispebjerg Hospital, Department of Dermatology D92, Bispebjerg Bakke 23, DK-2400 Copenhagen NV, Denmark

  33. 33

    The Laboratory of Cell Ultrastructure, Polish Academy of Sciences, Warsaw, Poland

  34. 34

    Department of Chemistry, SUNY, Binghamton, NY 13902-6016, USA

  35. 35

    Department of Cell Biology and Human Anatomy, School of Medicine, 1 Shields Avenue, Davis, CA 95616-8643, USA

  36. 36

    Department of Biological Chemistry, School of Medicine, 1 Shields Avenue, Davis, CA 95616-8643, USA

  37. 37

    Department of Biology, Tokyo Metropolitan University, Graduate School of Science, Hachioji, Tokyo 1920397, Japan

  38. 38

    Department of Biology, Tokyo Metropolitan University, Graduate School of Science, Hachioji, Tokyo 1920364, Japan

  39. 39

    Yale University School of Medicine and Howard Hughes Medical Institute, 310 Cedar St., PO Box 208011, New Haven, CT 06520-8011, USA

  40. 40

    The Roskamp Institute, University of South Florida, 3515 E. Fletcher Avenue, Tampa, FL 33613, USA

  41. 41

    Department of Molecular Pathology & Clinical Biochemistry, Royal Free Hospital Campus, Rowland Hill Street, London NW3 2PF, UK

  42. 42

    Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370, USA

  43. 43

    University of Leicester, Clinical Sciences Unit, Leicester General Hospital, Gwendolen Road, Leicester LE5 4PW, UK

  44. 44

    BBSRC Institute for Animal Health, High Street, Crompton RG20 7NN, UK

  45. 45

    Danish Center Society, Institute of Cancer Biology, Department of Molecular Cancer Biology, Strandblvd 49, 4-3, DK-2100 Copenhagen, Denmark

  46. 46

    Wellcome Trust Centre for Cell Matrix Research, School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester MI3 9PT, UK

  47. 47

    Institute of Zoology, Johannes Gutenberg-Universität, University of Mainz, D-55099 Mainz, Germany

  1. †

    deceased

Publication History

  1. Published Online: 3 JUL 2006
  2. Published Print: 27 JAN 2006

ISBN Information

Print ISBN: 9780470847589

Online ISBN: 9780470033487

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Keywords:

  • cell biology in vitro techniques;
  • nucleotide excision repair (NER) pathway;
  • halogen dU-substituted DNA;
  • nucleic acid metabolism;
  • single transporter recording;
  • Mitochondrial permeability transition (PT);
  • cytochrome cψ release;
  • SNARE (soluble NSF attachment protein receptor) proteins;
  • Human α-synuclein

Summary

This chapter contains sections titled:

  • Introduction

  • Nuclear components

  • Protocols 6.1 Nucleosome assembly coupled to DNA repair synthesis using a human cell free system

  • Protocols 6.2 Single labelling of nascent DNA with halogenated thymidine analogues

  • Protocols 6.3 Double labelling of DNA with different halogenated thymidine analogues

  • Protocols 6.4 Simultaneous immunostaining of proteins and halogen-dU-substituted DNA

  • Protocols 6.5 Uncovering the nuclear matrix in cultured cells

  • Protocols 6.6 Nuclear matrix–lamin interactions: in vitro blot overlay assay

  • Protocols 6.7 Nuclear matrix–lamin interactions: in vitro nuclear reassembly assay

  • Protocols 6.8 Preparation of Xenopus laevis egg extracts and immunodepletion

  • Protocols 6.9 Nuclear assembly in vitro and immunofluorescence

  • Protocols 6.10 Nucleocytoplasmic transport measurements using isolated Xenopus oocyte nuclei

  • Protocols 6.11 Transport measurements in microarrays of nuclear envelope patches by optical single transporter recording

  • Cells and membrane systems

  • Protocols 6.12 Cell permeabilization with Streptolysin O

  • Protocols 6.13 Nanocapsules: a new vehicle for intracellular delivery of drugs

  • Protocols 6.14 A rapid screen for determination of the protective role of antioxidant proteins in yeast

  • Protocols 6.15 In vitro assessment of neuronal apoptosis

  • Protocols 6.16 The mitochondrial permeability transition: PT and ΔΨm loss determined in cells or isolated mitochondria with confocal laser imaging

  • Protocols 6.17 The mitochondrial permeability transition: measuring PT and ΔΨmm loss in isolated mitochondria with Rh123 in a fluorometer

  • Protocols 6.18 The mitochondrial permeability transition: measuring PT and ΔΨmm loss in cells and isolated mitochondria on the FACS

  • Protocols 6.19 Measuring cytochrome c release in isolated mitochondria by Western blot analysis

  • Protocols 6.20 Protein import into isolated mitochondria

  • Protocols 6.21 Formation of ternary SNARE complexes in vitro

  • Protocols 6.22 In vitro reconstitution of liver endoplasmic reticulum

  • Protocols 6.23 Asymmetric incorporation of glycolipids into membranes and detection of lipid flip-flop movement

  • Protocols 6.24 Purification of clathrin-coated vesicles from rat brains

  • Protocols 6.25 Reconstitution of endocytic intermediates on a lipid monolayer

  • Protocols 6.26 Golgi membrane tubule formation

  • Protocols 6.27 Tight junction assembly

  • Protocols 6.28 Reconstitution of the major light-harvesting chlorophyll a/b complex into liposomes

  • Protocols 6.29 Reconstitution of photosystem 2 into liposomes

  • Protocols 6.30 Golgi–vimentin interaction in vitro and in vivo

  • Cytoskeletal and fibrillar systems

  • Protocols 6.31 Microtubule peroxisome interaction

  • Protocols 6.32 Detection of cytomatrix proteins by immunogold embedment-free electron microscopy

  • Protocols 6.33 Tubulin assembly induced by taxol and other microtubule assembly promoters

  • Protocols 6.34 Vimentin production, purification, assembly and study by EPR

  • Protocols 6.35 Neurofilament assembly

  • Protocols 6.36 α-Synuclein fibril formation induced by tubulin

  • Protocols 6.37 Amyloid-β fibril formation in vitro

  • Protocols 6.38 Soluble Aβ1−42 peptide induces tau hyperphosphorylation in vitro

  • Protocols 6.39 Anti-sense peptides

  • Protocols 6.40 Interactions between amyloid-β and enzymes

  • Protocols 6.41 Amyloid-β phosphorylation

  • Protocols 6.42 Smitin–myosin II coassembly arrays in vitro

  • Protocols 6.43 Assembly/disassembly of myosin filaments in the presence of EF-hand calcium-binding protein S100A4 in vitro

  • Protocols 6.44 Collagen fibril assembly in vitro

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