Flow Cytometry - First Principles (Second Edition)

HIV infection, CD34 stem cell enumeration, platelets, and transplantation cross-matching.

Van Dilla MA, Dean PN, Laerum OD, Melamed MR, eds. (1985). Flow Cytometry: Instrumentation and Data Analysis. Academic Press, London. A venerable, but still current book with an emphasis on the physics and mathematics of ¯ow systems and data analysis. It has some excellent (and readable) articles on some theoretical subjects.

Watson JV (1991). Introduction to Flow Cytometry. Cambridge University Press, Cambridge. A somewhat idiosyncratic tour through the many theoretical aspects of ¯ow cytometry with which Watson is well-acquainted. There are detailed discussions of the limits on signal resolution, on cell coincidence in the laser beam, and on methods for looking at dynamic cell events. There is also good coverage of oncological applications but no mention at all of lymphocytes.

Watson JV (1992). Flow Cytometry Data Analysis: Basic Concepts and Statistics. Cambridge University Press, Cambridge. A detailed look at the ways we can (or should) analyze dataÐafter we leave the ¯ow cytometer.

Weir DM, ed. (1986). Handbook of Experimental Immunology, Vol 1: Immunochemistry. Blackwell Scienti®c Publications, Oxford. A detailed reference volume on many aspects of immunology, including immuno¯uorescence techniques and antibody conjugation methods as well as ¯ow cytometric analysis. A newer edition (1996) of Weir's Handbook of Experimental Immunology (edited by Leonore Herzenberg) is also availableÐin four volumes.

CATALOGUES

The following are catalogues and handbooks from manufacturers. They are free and, even at ten times that price, would be well worth owning. Most are available in either paper or CD-ROM versions.

Melles Griot Catalog (http://www.mellesgriot.com/). This paper or CD guide provides a great deal of theoretical information about ®l- ter, lens, mirror, and laser speci®cations and design as well as about the Melles Griot range of products.

Molecular Probes: Handbook of Fluorescent Probes and Research Chemicals, by Richard P. Haugland. Molecular Probes (http:// www.molecularprobes.com/) makes a vast range of ¯uorescent chemicals that are useful in ¯ow cytometric analysis. The website and the paper or CD Handbook provide a great deal of information about the use of these chemicals as well as about their photochemical characteristics. A required reference book for every ¯ow cytometrist.

Hamamatsu Corporation (http://www.usa.hamamatsu.com/). This website contains a good discussion of photomultiplier tube electronics. We all need to be reminded occasionally that a ¯ow cytometer's performance is never any better than the performance of its photodetectors.

Boehringer Mannheim Biochemicals publishes a very useful manual on ``Apoptosis and Cell Proliferation.''

MISCELLANEOUS

The journal that specializes in research reports about ¯ow techniques and ¯ow analysis (as well as image analyis) is Cytometry. Its paired publication is Communications in Clinical Cytometry. The Journal of Immunological Methods is also often useful in this regard.

The International Society for Analytical Cytometry (ISAC, 60 Revere Drive, Suite 500, Northbrook, IL 60062; http://www.isac-net.org) is the society that specializes in ¯ow and image cell analysis. Meetings (attended by about 1000 people) are held every 2 years (sometimes in the United States and sometimes in Europe).

The U.S. National Flow Cytometry Resource is at the Los Alamos National Laboratory (Los Alamos, NM 87545). They are a source of information and inspiration and provide help and facilities for scientists wanting to make use of their ``state-of-the art'' cytometers. They also run ¯ow cytometry training courses.

Websites on ¯ow cytometry re¯ect the idiosyncracies of their authors. Many are excellent. For current listings of this ever-changing scene, search the Purdue University Cytometry Laboratories website (http:// www.cyto.purdue.edu/) or the ISAC web site (http://www.isac-net. org/).

There is an e-mail network for informal discussion on ¯ow issues. It has, as of this writing, 1999 members. Participants in this network are a singularly helpful and generous group of people. The network is run by Paul Robinson and Steve Kelley from Purdue University. Sign up by writing to Steve Kelley (cyto-request@¯owcyt.cyto.purdue.edu).

Courses on ¯ow cytometry are held at various locations, mainly during the summer. For current listings check the Purdue website (http://www.cyto.purdue.edu/), which is usually as up-to-date as possible.

Fig. 5.6. Reprinted with permission of John Wiley & Sons, Inc. ( 1995 from Shapiro HM (1995). Practical Flow Cytometry, 3rd edition. New York: Wiley-Liss.

Fig. 5.7. Reprinted from Givan AL (2001). Principles of ¯ow cytometry: an overview. Darzynkiewicz Z, et al. (eds). Cytometry, 3rd edition. San Diego: Academic Press, pp 19±50.

Fig. 6.1. Reprinted from Kessel RG and Kardon RH (1979). Tissues and Organs: a Text-Atlas of Scanning Electron Microscopy. San Francisco: WH Freeman & Co.

Fig. 6.3. Printed with permission from Ian Brotherick.

Fig. 6.6. Reprinted from Givan AL (2001). Principles of ¯ow cytometry: an overview. Darzynkiewicz Z, et al. (eds). Cytometry, 3rd edition. San Diego: Academic Press, pp 19±50.

Fig. 6.15. Reprinted with permission of John Wiley & Sons, Inc. ( 2000 from Loken MR and Wells DA (2000). Normal antigen expression in hematopoiesis. Stewart CC and Nicholson JKA (eds). Immunophenotyping. New York: Wiley-Liss, pp 133±160.

Fig. 6.17. Reprinted from Horan PK, et al. (1986). Improved ¯ow cytometric analysis of leucocyte subsets: simultaneous identi®cation of ®ve cell subsets using twocolor immuno¯uorescence. Proc. Natl. Acad. Sci. 83:8361±8363.

Fig. 7.1. Unpublished results from McNally A and Bauer KD, reprinted with permission from Bauer KD and Jacobberger JW (1994). Analysis of intracellular proteins. Darzynkiewicz Z, et al (eds). Flow Cytometry, 2nd edition. San Diego: Academic Press, pp 351±376.

Fig. 7.3. Reprinted (in modi®ed form) with permission of John Wiley & Sons, Inc. ( 1995 from Brotherick I, et al (1995). Use of the biotinylated antibody DAKO-ER 1D5 to measure oestrogen receptors on cytokeratin positive cells obtained from primary breast cancer cells. Cytometry 20:74±80.

Fig. 8.3. Reprinted from Alberts B, et al. (1989). Molecular Biology of the Cell, 2nd edition. New York: Garland Publishing.

Fig. 8.4. Reprinted with permission of John Wiley & Sons, Inc. ( 1990 from Gray JW, et al. (1990). Quantitative cell-cycle analysis. Melamed MR, et al. (eds). Flow Cytometry and Sorting. New York: Wiley-Liss, pp 445±467. The work was performed at the University of California Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy.

Fig. 8.7. Reprinted (A,D) from Dean PN (1987). Data analysis in cell kinetics. Gray JW and Darzynkiewicz Z (eds). Techniques in Cell Cycle Analysis. Clifton, NJ: Humana Press, pp 207±253; and (B,C) from Dean PN (1985). Methods of data analysis in ¯ow cytometry. Van Dilla MA, et al. (eds). Flow Cytometry: Instrumentation and Data Analysis. London: Academic Press, pp 195±221.

Fig. 8.9. Reprinted with permission of John Wiley & Sons, Inc. ( 1989 from Peeters JCH, et al. (1989). Optical plankton analyser. Cytometry 10:522±528.

Fig. 8.10. Reprinted in modi®ed form with permission from Michael Ormerod.

Fig. 8.13. Reprinted with permission of Oxford University Press from McNally NJ and Wilson GD (1990). Measurement of tumour cell kinetics by the bromodeoxyuridine method. Ormerod MG (ed). Flow Cytometry: A Practical Approach. Oxford: IRL, pp 87±104.

Fig. 8.14. Reprinted with permission of John Wiley & Sons, Inc. ( 1990 from Darzynkiewicz Z and Traganos F (1990). Multiparameter ¯ow cytometry studies of the cell cycle. Melamed MR, et al. (eds). Flow Cytometry and Sorting. New York: Wiley-Liss, pp 469±501.

Fig. 8.15. Reprinted with permission of John Wiley & Sons, Inc. ( 1990 from Darzynkiewicz Z (1990). Probing nuclear chromatin by ¯ow cytometry. Melamed MR, et al. (eds). Flow Cytometry and Sorting. New York: Wiley-Liss, pp 315± 340.

Fig. 8.17. Reprinted with permission of John Wiley & Sons, Inc. ( 1998 from Juan G, et al. (1998). Histone H3 phosphorylation and expression of cyclins A and B1 measured in individual cells during their progression through G2 and mitosis.

Cytometry 32:71±77.

Fig. 8.18. Printed with permission from James Jacobberger.

Fig. 8.19. Reprinted with permission of John Wiley & Sons, Inc. ( 1988 from Cram LS, et al. (1988). Overview of ¯ow cytogenetics for clinical applications. Cytometry [suppl] 3:94±100.

Fig. 8.20. Reprinted with permission of John Wiley & Sons, Inc. ( 1990 from Gray JW and Cram LS (1990). Flow karyotyping and chromosome sorting. Melamed MR, et al. (eds). Flow Cytometry and Sorting. New York: Wiley-Liss, pp 503± 529. The work was performed at the University of California Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy.

Fig. 8.21. Reprinted with permission of John Wiley & Sons, Inc. ( 1990 from Gray JW and Cram LS (1990). Flow karyotyping and chromosome sorting. Melamed MR, et al. (eds). Flow Cytometry and Sorting. New York: Wiley-Liss, pp 503±529. The work was performed at the University of California Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy.

Fig. 9.1. Reprinted from Cytomation, Inc., Fort Collins, CO.

Fig. 10.1. Printed with permission from Ben Givan.

Fig. 10.2. Reprinted with permission of John Wiley & Sons, Inc. ( 2000 from Loken MR and Wells DA (2000). Normal antigen expression in hematopoiesis. Stewart CC and Nicholson JKA (eds). Immunophenotyping. New York: Wiley-Liss, pp 133±160.

Fig. 10.3. Printed with permission from Carleton Stewart.

Fig. 10.4. Printed with permission from LeÂonie Walker.

Fig. 10.5. Unpublished results from Sutherland R, reprinted with permission of John Wiley & Sons, Inc. ( 2000 from Gee AP and Lamb LS Jr (2000). Enumeration of CD34-positive hematopoietic progenitor cells. Stewart CC and Nicholson JKA (eds). Immunophenotyping. New York: Wiley-Liss, pp 291±319.

Fig. 10.6. From Davis BH et al (1998). Detection of fetal red cells in fetomaternal hemorrhage using a fetal hemoglobin monoclonal antibody by ¯ow cytometry. Reprinted with permission from Transfusion 38:749±756, published by the American Association of Blood Banks.

Fig. 10.7. Reprinted from Yuan J, Hennessy C, et al. (1991). Node negative breast cancer: the prognostic value of DNA ploidy for long-term survival. British J. Surg. 78:844±848.

Fig. 11.1. Reprinted (with modi®cations) with permission of John Wiley & Sons, Inc. ( 1995 from Shapiro HM (1995). Practical Flow Cytometry, 3rd edition. New York: Wiley-Liss.

Fig. 11.5. Reprinted from Veldhuis MJW and Kraay GW (2000). Application of ¯ow cytometry in marine phytoplankton research: current applications and future perspectives. Scientia Marina 64:121±134.

Fig. 11.6. Reprinted with permission of the Department of Fisheries and Oceans and the Minister of Supply and Services, Canada, 1991, from Chisholm S, et al. (1986). The individual cell in phytoplankton ecology. Can. Bull. Fish. Aquat. Sci. 214:343± 369.

Fig. 11.7. Printed with permission of Sandra Shumway.

Fig. 11.8. Reprinted with permission of YN Jan from Bier E, et al. (1989). Searching for pattern and mutation in the Drosophila genome with a P-lac Z vector. Genes and Dev. 3:1273±1287.

Fig. 11.9. Printed with permission from Mark Krasnow.

Fig. 11.10. Reprinted with permission from Krasnow M, et al. (1991). Whole animal cell sorting of Drosophila embryos. Science 251:81±85. ( 1991 by the American Association for the Advancement of Science.

Fig. 11.11. Reprinted from Weaver JC (1990). Sampling: a critical problem in biosensing. Med. Biol. Eng. Comput. 28:B3±B9.

Fig. 11.12. Reprinted from Weaver JC, et al. (1991). Rapid clonal growth measurements at the single cell level: gel microdroplets and ¯ow cytometry. Bio/Technology 9:873.

Fig. 11.13. Reprinted with permission of John Wiley & Sons, Inc. ( 1990 from Van Dilla M, et al. (1990). Applications of ¯ow cytometry and sorting to molecular genetics. Melamed MR, et al. (eds). Flow Cytometry and Sorting. New York: WileyLiss, pp 562±604.

Fig. 11.14. Reprinted with permission of John Wiley & Sons, Inc. ( 1999 from Kim Y, et al. (1999). Bacterial ®ngerprinting by ¯ow cytometry: bacterial species discrimination. Cytometry 36:324±332.

Fig. 11.15. Reprinted (with modi®cations) with permission from Elsevier Science (Copyright 1999) from Carson RT and Vignali DAA (1999). Simultaneous quantitation of 15 cytokines using a multiplexed ¯ow cytometric assay. J. Immunol. Methods 227:41±52.

Acridine orange: Acridine orange (AO) is a stain that ¯uoresces either red or green, depending on whether it is bound to doublestranded or single-stranded nucleic acid. It has proved useful in comparing DNA and RNA content within cells; and it has also been used successfully (in the presence of RNase and mild denaturing conditions) to look at the changes in DNA denaturability during the cell cycle. There is debate in the ¯ow cytometric community about whether the reputation that AO has for being di½cult to work with is justi®ed.

Activation marker: Activation markers are proteins that come and go on the surface of cells in response to stimulation. As such, they provide functional information about the physiological state of the cell. They also provide ¯ow cytometrists with a reason to be concerned about instrument stability, sensitivity, and standardization.

ADC: An analog-to-digital converter converts photodetector signals (called analog signals because they are continuously variable, having an in®nite variety of values) to channel numbers. The light intensity range represented by a given ADC channel depends on the ampli®cation applied to the photodetector signal. ADCs can have 256 or 1024 or even 65,536 channels.

Aerosol: An aerosol is the spray of small ¯uid droplets that can be generated particularly when the nozzle of a ¯ow cytometer is vibrated for sorting applications. If samples contain material that may be a biological hazard, attention should be paid to containment of the aerosol by suction through small-pore, hydrophobic ®lters.

Algae: Algae are simple forms of plant life. The larger algae are known as seaweeds. The unicellular algae form a large part of the plankton of both marine and fresh water environments and are suitable for analysis by ¯ow cytometers. Algae also have contributed greatly to ¯ow cytometric analysis because of their elaboration of pigments like phycoerythrin, PerCP, and allophycocyanin, which can be conjugated to antibodies and which facilitate multicolor staining procedures because they ¯uoresce in di¨erent regions of the spectrum.