Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

564 Chapter 9: Visualizing Cells
separated. When the CFP and YFP domains are brought
close together, however, fluorescence resonance energy
transfer (FRET) allows excitation of CFP to stimulate emission
by YFP. FRET shows up experimentally as an increase
in the ratio of emission at 526 nm versus 476 nm (YFP/
CFP) when CFP is excited by 434 nm light.
Incubation of the reporter protein with Abl protein
tyrosine kinase in the presence of ATP gave an increase
in YFP/CFP emission (Figure Q9–4B). In the absence of
ATP or the Abl protein, no FRET occurred. FRET was also
eliminated by addition of a tyrosine phosphatase (Figure
Q9–4B). Describe as best you can how the reporter protein
detects active Abl protein tyrosine kinase.
REFERENCES
General
Celis JE, Carter N, Simons K et al. (eds) (2005) Cell Biology:
A Laboratory Handbook, 3rd ed. San Diego: Academic Press.
(Volume 3 of this four-volume set covers the practicalities of most
of the current light and electron imaging methods that are used in
cell biology.)
Pawley BP (ed) (2006) Handbook of Biological Confocal Microscopy,
3rd ed. New York: Springer Science.
Wayne R (2014) Light and Video Microscopy. San Diego: Academic
Press.
Looking at Cells in the Light Microscope
Adams MC, Salmon WC, Gupton SL et al. (2003) A high-speed
multispectral spinning-disk confocal microscope system for
fluorescent speckle microscopy of living cells. Methods 29, 29–41.
Agard DA, Hiraoka Y, Shaw P & Sedat JW (1989) Fluorescence
microscopy in three dimensions. In Methods in Cell Biology, Vol. 30:
Fluorescence Microscopy of Living Cells in Culture, part B
(DL Taylor, Y-L Wang eds). San Diego: Academic Press.
Burnette DT, Sengupta P, Dai Y et al. (2011) Bleaching/blinking assisted
localization microscopy for superresolution imaging using standard
fluorescent molecules. Proc. Natl Acad. Sci. USA 108,
21081–21086.
Chalfie M, Tu Y, Euskirchen G et al. (1994) Green fluorescent protein as
a marker for gene expression. Science 263, 802–805.
Giepmans BN, Adams SR, Ellisman MH & Tsien RY (2006) The
fluorescent toolbox for assessing protein location and function.
Science 312, 217–224.
Harlow E & Lane D (1998) Using Antibodies: A Laboratory Manual. Cold
Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
Hell S (2009) Microscopy and its focal switch. Nat. Methods 6, 24–32.
Huang B, Babcock H & Zhuang X (2010) Breaking the diffraction
barrier: super-resolution imaging of cells. Cell 143, 1047–1058.
Huang B, Bates M & Zhuang X (2009) Super-resolution fluorescence
microscopy. Annu. Rev. Biochem. 78, 993–1016.
Jaiswai JK & Simon SM (2004) Potentials and pitfalls of fluorescent
quantum dots for biological imaging. Trends Cell Biol. 14, 497–504.
Klar ta, Jakobs S, Dyba M et al. (2000) Fluorescence microscopy with
diffraction resolution barrier broken by stimulated emission. Proc.
Natl Acad. Sci. USA 97, 8206–8210.
Lippincott-Schwartz J & Patterson GH (2003) Development and use of
fluorescent protein markers in living cells. Science 300, 87–91.
Lippincott-Schwartz J, Altan-Bonnet N & Patterson G (2003)
Photobleaching and photoactivation: following protein dynamics in
living cells. Nat. Cell Biol. 5(Suppl), S7–S14.
McEvoy AL, Greenfield D, Bates M & Liphardt J (2010) Q&A: Singlemolecule
localization microscopy for biological imaging. BMC Biol.
8, 106.
Minsky M (1988) Memoir on inventing the confocal scanning
microscope. Scanning 10, 128–138.
Miyawaki A, Sawano A & Kogure T (2003) Lighting up cells: labelling
proteins with fluorophores. Nat. Cell Biol. 5(Suppl), S1–S7.
Parton RM & Read ND (1999) Calcium and pH imaging in living cells. In
Light Microscopy in Biology. A Practical Approach, 2nd ed. (Lacey
AJ ed.). Oxford: Oxford University Press.
Patterson G, Davidson M, Manley S & Lippincott-Schwartz J (2010)
Superresolution imaging using single-molecule localization. Annu.
Rev. Phys. Chem. 61, 345–367.
Rust MJ, Bates M & Zhuang X (2006) Sub-diffraction-limit imaging
by stochastic optical reconstruction microscopy (STORM). Nat.
Methods 3, 793–795.
Sako Y & Yanagida T (2003) Single-molecule visualization in cell biology.
Nat. Rev. Mol. Cell Biol. 4(Suppl), SS1–SS5.
Schermelleh L, Heintzmann R & Leonhardt H (2010) A guide to superresolution
fluorescence microscopy. J. Cell Biol. 190, 165–175.
Shaner NC, Steinbach pa & Tsien RY (2005) A guide to choosing
fluorescent proteins. Nat. Methods 2, 905–909.
Sluder G & Wolf DE (2007) Digital Microscopy, 3rd ed: Methods in Cell
Biology, Vol 81. San Diego: Academic Press.
Stephens DJ & Allan VJ (2003) Light microscopy techniques for live cell
imaging. Science 300, 82–86.
Tsien RY (2008) Constructing and exploiting the fluorescent protein
paintbox. Nobel Prize Lecture. www.nobelprize.org
White JG, Amos WB & Fordham M (1987) An evaluation of confocal
versus conventional imaging of biological structures by
fluorescence light microscopy. J. Cell Biol. 105, 41–48.
Zernike F (1955) How I discovered phase contrast. Science
121, 345–349.
Looking at Cells and Molecules in the Electron
Microscope
Allen TD & Goldberg MW (1993) High-resolution SEM in cell biology.
Trends Cell Biol. 3, 205–208.
Baumeister W (2002) Electron tomography: towards visualizing the
molecular organization of the cytoplasm. Curr. Opin. Struct. Biol.
12, 679–684.
Böttcher B, Wynne SA & Crowther RA (1997) Determination of the fold
of the core protein of hepatitis B virus by electron cryomicroscopy.
Nature 386, 88–91.
Dubochet J, Adrian M, Chang J-J et al. (1988) Cryo-electron
microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228.
Frank J (2003) Electron microscopy of functional ribosome complexes.
Biopolymers 68, 223–233.
Frank J (2009) Single-particle reconstruction of biological
macromolecules in electron microscopy—30 years. Quart. Rev.
Biophys. 42, 139–158.
Hayat MA (2000) Principles and Techniques of Electron Microscopy,
4th ed. Cambridge: Cambridge University Press.
Heuser J (1981) Quick-freeze, deep-etch preparation of samples for
3-D electron microscopy. Trends Biochem. Sci. 6, 64–68.
Liao M, Cao E, Julius D & Cheng Y (2014) Single particle electron
cryo-microscopy of a mammalian ion channel. Curr. Opin. Struct.
Biol. 27, 1–7.
Lucic V, Förster F & Baumeister W (2005) Structural studies by electron
tomography: from cells to molecules. Annu. Rev. Biochem. 74,
833–865.
McDonald KL & Auer M (2006) High-pressure freezing, cellular
tomography, and structural cell biology. Biotechniques 41,
137–139.
McIntosh JR (2007) Cellular Electron Microscopy. 3rd ed: Methods in
Cell Biology, Vol 79. San Diego: Academic Press.
McIntosh R, Nicastro D & Mastronarde D (2005) New views of cells in
3D: an introduction to electron tomography. Trends Cell Biol.
15, 43–51.
Pease DC & Porter KR (1981) Electron microscopy and ultramicrotomy.
J. Cell Biol. 91, 287s–292s.
Unwin PNT & Henderson R (1975) Molecular structure determination
by electron microscopy of unstained crystalline specimens. J. Mol.
Biol. 94, 425–440.
Zhou ZH (2008) Towards atomic resolution structural determination buy
single particle cryo-electron microscopy. Curr. Opin. Struct. Biol.
18, 218–228.