Essential Numerical Computer Methods

Edited by

  • Michael Johnson, University of Virginia Health Sciences Center, Charlottesville, USA

The use of computers and computational methods has become ubiquitous in biological and biomedical research. During the last 2 decades most basic algorithms have not changed, but what has is the huge increase in computer speed and ease of use, along with the corresponding orders of magnitude decrease in cost.

A general perception exists that the only applications of computers and computer methods in biological and biomedical research are either basic statistical analysis or the searching of DNA sequence data bases. While these are important applications they only scratch the surface of the current and potential applications of computers and computer methods in biomedical research. The various chapters within this volume include a wide variety of applications that extend far beyond this limited perception. As part of the Reliable Lab Solutions series, Essential Numerical Computer Methods brings together chapters from volumes 210, 240, 321, 383, 384, 454, and 467 of Methods in Enzymology. These chapters provide a general progression from basic numerical methods to more specific biochemical and biomedical applications.

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Biochemists, biophysicists, physical chemists, molecular biologists, cell biologists


Book information

  • Published: October 2010
  • ISBN: 978-0-12-384997-7

Table of Contents

Part I: Fluorochromes/General Techniques
1. Principles of confocal microscopy (Robinson)
2. Protein labeling with fluorescent probes (Holmes, Lantz)
3. Cytometry of fluorescence resonance energy transfer (Vereb, Matko, Szollosi)
4. The rainbow of fluorescent proteins (Galbraith)
5. Labeling cellular targets with semiconductor quantum dot conjugates (Wu, Bruchez)
6. High-gradient magnetic cell sorting (Radbruch, Mechtold, Thiel, Miltenyi, Pfluger)
7. Multiplexed microsphere assays for protein and DNA binding reactions (Kellar, Oliver)
8. Biohazard sorting (Schmid, Roederer, Koup, Ambrozak, Perfetto)
9. Guidelines for the presentation of flow cytometric data. (Roederer, Darzynkiewicz, Paks)
Part II: Cellular DNA Content Analysis
10. VinDetergent and proteolytic enzyme-based techniques for nuclear isolation and DNA content analysis.(Vindelov,Christensen)
11. Rapid DNA content analysis (Krishan)
12. DNA analysis from paraffin-embedded blocks. (Hedley)
13. Flow cytometry and sorting of plant protoplasts and cells (Galbraith)
14. DNA content histogram and cell cycle analysis. (Rabinovitch)
15. Simultaneous analysis of cellular RNA and DNA content (Darzynkiewicz)
Part III. Cell Proliferation and Death Assays
16. Immunochemical quantitation of bromodeoxyuridine: application to cell cycle kinetics (Dolbeare, Selden)|
17. Cell cycle kinetics estimated by analysis of bromodeoxyuridine incorporation (Terry, White)
18. Flow cytometric analysis of cell division history using dilution of carboxyfluorescein diacetate succinimidyl ester, a stably integrated fluorescent probe. (Lyons, Hasbold, Hodgkin)
19. Antibodies against the Ki-67 protein: Assessment of the growth fraction and tools for cell cycle analysis (Endl, Hollman, Gerdes)
20. Detection of DNA damage in individual cells by analysis of histone H2AX phosphorylation (Olive)
21. Assays of cell viability: Discrimination of cells dying by apoptosis. (Darzynkiewicz, Li, Gong)
22. Difficulties and pitfalls in analysis of apoptosis (Darzynkiewicz, Bedner, Traganos)
Part IV: Cell Surface Immunophenotyping
23. Cell preparation for the identification of leukocytes (Stewart, Stewart)
24. Multicolor immunophenotyping: Human immune system hematopoiesis (Wood)
25. Differential diagnosis of T-cell lymphoproliferative disorders by flow cytometry multicolor immunophenotyping. Correlation with morphology. (Gorczyca)
26. B-cell immunophenotyping (Baumgarth)
Part V: Cytogenetics/Chromatin Structure
27. Telomere length measurements using in situ hybridization(Baerlocher, Lansdorp)
28. Sperm chromatin structure assay: DNA denaturability (Evanson, Jost)
Part VI: Cell Physiology Assays
29. Cell membrane potential analysis. (Shapiro)
30. Measurement of intracellular pH. (Boyer, Hedley)
31. Intracellular ionized calcium (June, Rabinovitch)
32. Oxidative product formation analysis by flow cytometry (Robinson, Carter, Narayanan).
33. Phagocyte function. (Rothe, Glouche)
34. Analysis of RNA synthesis by cytometry (Jensen, Larsen, Larsen)
35. Analysis of mitochondria by flow cytometry (Poot, Pierce)
36. Analysis of platelets by flow cytometry (Ault, Mitchell)
Part VII: Detection of Microorganisms and Pathogens
37. Detection of specific microorganisms in environmental samples using flow cytometry (Vesey, Narai, Ashbolt, Williams, Veal)
38. Flow cytometric analysis of microorganisms. (Sincock, Robinson)
39. Flow cytometry of malaria detection (Janse, Van Vianen)