Design of experiments (DOE)—history, concepts, and relevance to in vitro culture

In Vitro Cellular and Developmental Biology - Plant

Volumn 52, Issue 6, 2016, Pages 547-562

  Niedz, Randall P ^a   Evens, Terence J ^a  

^a U S HORTICULTURAL RESEARCH LABORATORY   (United States)

Author keywords

Experimental design; Ion specific effects; Mineral nutrition; Plant tissue culture; Scientific method

Indexed keywords

EID: 84987653128     PISSN: 10545476     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11627-016-9786-1     Document Type: Review

References (65)

1. Aarts AA, Anderson JE, Anderson CJ, Attridge PR, Attwood A, Axt J, Babel M, Bahník Š, Baranski E, Barnett-Cowan M, Bartmess E, Beer J, Bell R, Bentley H, Beyan L, Binion G, Borsboom D, Bosch A, Bosco FA, Bowman SD, Brandt MJ, Braswell E, Brohmer H, Brown BT, Brown K, Brüning J, Calhoun-Sauls A, Callahan SP, Chagnon E, Chandler J, Chartier CR, Cheung F, Christopherson CD, Cillessen L, Clay R, Cleary H, Cloud MD, Conn M, Cohoon J, Columbus S, Cordes A, Costantini G, Alvarez LDC, Cremata E, Crusius J, DeCoster J, DeGaetano MA, Penna ND, Den Bezemer B, Deserno MK, Devitt O, Dewitte L, Dobolyi DG, Dodson GT, Donnellan MB, Donohue R, Dore RA, Dorrough A, Dreber A, Dugas M, Dunn EW, Easey K, Eboigbe S, Eggleston C, Embley J, Epskamp S, Errington TM, Estel V, Farach FJ, Feather J, Fedor A, Fernández-Castilla B, Fiedler S, Field JG, Fitneva SA, Flagan T, Forest AL, Forsell E, Foster JD, Frank MC, Frazier RS, Fuchs H, Gable P, Galak J, Galliani EM, Gampa A, Garcia S, Gazarian D, Gilbert E, Giner-Sorolla R, Glöckner A, Goellner L, Goh JX, Goldberg R, Goodbourn PT, Gordon-McKeon S, Gorges B, Gorges J, Goss J, Graham J, Grange JA, Gray J, Hartgerink C, Hartshorne J, Hasselman F, Hayes T, Heikensten E, Henninger F, Hodsoll J, Holubar T, Hoogendoorn G, Humphries DJ, Hung COY, Immelman N, Irsik VC, Jahn G, Jäkel F, Jekel M, Johannesson M, Johnson LG, Johnson DJ, Johnson KM, Johnston WJ, Jonas K, Joy-Gaba JA, Kappes HB, Kelso K, Kidwell MC, Kim SK, Kirkhart M, Kleinberg B, Knežević G, Kolorz FM, Kossakowski JJ, Krause RW, Krijnen J, Kuhlmann T, Kunkels YK, Kyc MM, Lai CK, Laique A, Lakens D, Lane KA, Lassetter B, Lazarević LB, Le Bel EP, Lee KJ, Lee M, Lemm K, Levitan CA, Lewis M, Lin L, Lin S, Lippold M, Loureiro D, Luteijn I, MacKinnon S, Mainard HN, Marigold DC, Martin DP, Martinez T, Masicampo EJ, Matacotta J, Mathur M, May M, Mechin N, Mehta P, Meixner J, Melinger A, Miller JK, Miller M, Moore K, Möschl M, Motyl M, Müller SM, Munafo M, Neijenhuijs KI, Nervi T, Nicolas G, Nilsonne G, Nosek BA, Nuijten MB, Olsson C, Osborne C, Ostkamp L, Pavel M, Penton-Voak IS, Perna O, Pernet C, Perugini M, Pipitone RN, Pitts M, Plessow F, Prenoveau JM, Rahal RM, Ratliff KA, Reinhard D, Renkewitz F, Ricker AA, Rigney A, Rivers AM, Roebke M, Rutchick AM, Ryan RS, Sahin O, Saide A, Sandstrom GM, Santos D, Saxe R, Schlegelmilch R, Schmidt K, Scholz S, Seibel L, Selterman DF, Shaki S, Simpson WB, Sinclair HC, Skorinko JLM, Slowik A, Snyder JS, Soderberg C, Sonnleitner C, Spencer N, Spies JR, Steegen S, Stieger S, Strohminger N, Sullivan GB, Talhelm T, Tapia M, Te Dorsthorst A, Thomae M, Thomas SL, Tio P, Traets F, Tsang S, Tuerlinckx F, Turchan P, Valášek M, Van't Veer AE, Van Aert R, Van Assen M, Van Bork R, Van De Ven M, Van Den Bergh D, Van Der Hulst M, Van Dooren R, Van Doorn J, Van Renswoude DR, Van Rijn H, Vanpaemel W, Echeverría AV, Vazquez M, Velez N, Vermue M, Verschoor M, Vianello M, Voracek M, Vuu G, Wagenmakers EJ, Weerdmeester J, Welsh A, Westgate EC, Wissink J, Wood M, Woods A, Wright E, Wu S, Zeelenberg M, Zuni K (2015) Estimating the reproducibility of psychological science. Science 349(6251). doi:10.1126/science.aac4716
2. Anderson DM, Cembella AD, Hallegraeff GM (2012) Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management. Ann Rev Mar Sci 4:143–176
3. Andersson R, Eriksson H, Torstensson H (2006) Similarities and differences between TQM, six sigma and lean. The TQM Magazine 18:282–296
4. Bacon F (1650) Novum organum scientiarum. Adriani Wyngaerden, London
5. Bailey NTJ (1967) The mathematical approach to biology and medicine. John Wiley & Sons, London, New York, Sydney xiii, pg. 23
6. Barker TB (1986) Quality engineering by design: Taguchi's philosophy. Quality Progress 19:32–42
7. Bayart D (2001) Walter Andrew Shewhart. In: Heyde CC, Seneta E (eds) Statisticians of the centuries. Springer-Verlag, New York, pp. 398–401
8. Begley CG, Ioannidis JP (2015) Reproducibility in science: improving the standard for basic and preclinical research. Circ Res 116:116–126
9. Box JF (1978) R.A. Fisher: the life of a scientist. Wiley, New York
10. Box GEP, Meyer RD (1986) An analysis for unreplicated fractional factorials. Technometrics 28:11–18
11. Box GEP, Wilson KB (1951) On the experimental attainment of optimum conditions. Journal of the Royal Statistical Society Series B (Methodological) 13:1–45
12. Chernoff H (1999) Gustav Elfving's impact on experimental design. Stat Sci 14:201–205
13. Chu CC, Wang CS, Sun CS, Hsu V, Yin KC, Chu CY, Bi FY (1975) Establishment of an efficient medium for anther culture of rice through experiments on the nitrogen source. Scient Sin 18:659– 668
14. Collins FS, Tabak LA (2014) NIH plans to enhance reproducibility. Nature 505:612–613
15. Davidson K, Gowen RJ, Tett P, Bresnan E, Harrison PJ, McKinney A, Milligan S, Mills DK, Silke J, Crooks AM (2012) Harmful algal blooms: how strong is the evidence that nutrient ratios and forms influence their occurrence? Estuar Coast Shelf Sci 115:399–413
16. DeLoach R (2000) Improved quality in aerospace testing through the modern design of experiments. 38th Aerospace Sciences Meeting and Exhibit. American Institute of Aeronautics and Astronautics, Reston, Virginia
17. DeLoach R (2002) The objective of aerospace ground testing: an alternative perspective. GTTC Newsletter 5:18–19
18. DeLoach R (2010) Analysis of variance in the modern design of experiments. 48th AIAA Aerospace Sciences Meeting Including the New Horizons Forum and Aerospace Exposition. American Institute of Aeronautics and Astronautics, Orlando, Florida
19. Deming WE (2000) The new economics for industry, government, education, 2nd edn. MIT Press, Cambridge, Massachusetts
20. Driver JA, Kuniyuki AM (1984) In vitro propagation of Paradox walnut rootstock. HortSci 19:507–509
21. Evens TJ, Niedz RP (2008) Are Hofmeister series relevant to modern ion-specific effects research? Scholarly Research Exchange. doi:10.3814/2008/761829
22. Evens TJ, Niedz RP (2011) Mapping the fundamental niches of two freshwater microalgae, Chlorella vulgaris (Trebouxiophyceae) and Peridinium cinctum (Dinophyceae), in 5-dimensional ion space. Int J Ecol 2011:1–12
23. Feynman RP, Leighton RB, Sands M (1963) The Feynman Lectures on Physics. Addison-Wesley Publishing Company, Reading, MA
24. Fisher RA (1921) Studies in crop variation. I. An examination of the yield of dressed grain from Broadbalk. J Agric Sci 11:107–135
25. Fisher RA (1925) Statistical methods for research workers. Oliver and Boyd, Edinburgh
26. Fisher RA (1926) The arrangement of field experiments. J Minist Agric (GB) 33:503–513
27. Fisher RA (1937) The design of experiments, 2nd edn. Oliver and Boyd, Edinburgh
28. Fisher RA (1947) Development of the theory of experimental design. Proceedings of the International Statistical Conferences (Washington) 3:434–439
29. Fisher RA (1952) Statistical methods in genetics. Heredity 6:1–12
30. Freedman LP, Cockburn IM, Simcoe TS (2015) The economics of reproducibility in preclinical research. PLoS Biol 13:e1002165
31. Gaither CC, Cavazos-Gaither AE (2012) Gaither’s dictionary of scientific quotations, 2nd edn. Springer, New York
32. Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151–158
33. George EF (1993) Plant propagation by tissue culture. Part 1: The technology, 2nd edn. Exegetics Limited, Edington, UK
34. Glibert PM, Burkholder JM (2011) Harmful algal blooms and eutrophication: "strategies" for nutrient uptake and growth outside the Redfield comfort zone. Chin J Oceanol Limnol 29:724–738
35. Hallegraeff GM (2010) Ocean climate change, phytoplankton community responses, and harmful algal blooms: a formidable predictive challenge. J Phycol 46:220–235
36. Heller R (1953) Researches on the mineral nutrition of plant tissues. Ann Sci Nat Bot Biol Vég, 11th Ser 14:1–223
37. Johnston AE, Garner HV (1969) Broadbalk: historical introduction. Rothamsted Experimental Station Report for 1968 Part 2:12–25
38. Knop W (1865) Quantitative Utersuchungen Über den Ernährungensprozeß der Pflanze. Landw Versuchssat 7:93–107
39. Knudson L (1943) Nutrient solutions for orchid seed germination. Am Orchid Soc Bull 12:77–79
40. Kuhfeld WF (2010) Experimental design: efficiency, coding, and choice designs. Available via https://support.sas.com/techsup/technote/mr2010c.pdf
41. Landsberg JH (2002) The effects of harmful algal blooms on aquatic organisms. Rev Fish Sci 10:113–390
42. Larsen K (2005) Stephen Hawking: a biography. Greenwood Press, Westport, Connecticut, p. 43
43. Lloyd G, McCown B (1980) Commercially-feasible micropropagation of mountain laurel, Kalmia latifolia, by use of shoot tip culture. Proc Int Plant Propagators Soc 30:421–427
44. McGranahan GH, Driver JA, Tulecke W (1987) Tissue culture of Juglans. In: Bonga JM, Durzan DJ (eds) Cell and tissue culture in forestry: case histories: gymnosperms, angiosperms and palms. Springer Netherlands, Dordrecht, pp. 261–271
45. Montgomery DC (2013) Design and analysis of experiments, 8th edn. Wiley, Hoboken, NJ
46. Morel G, Muller J F (1964) La culture in vitro du merstem apical de la pommede terre. Compt Rend Acad Sci 258:5255–5250
47. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497
48. Niedz RP, Evens TJ (2006) A solution to the problem of ion confounding in experimental biology. Nat Methods 3:417
49. Niedz RP, Evens TJ (2007) Regulating plant tissue growth by mineral nutrition. In Vitro Cell Dev Biol Plant 43:370–381
50. Niedz RP, Evens TJ (2011) Mixture screening and mixture-amount designs to determine plant growth regulator effects on shoot regeneration from grapefruit (Citrus paradisi macf.) epicotyls. In Vitro Cell Dev Biol Plant 47:682–694
51. Nitsch JP, Nitsch C (1969) Haploid plants from pollen grains. Science 163:85–87
52. Nordström K (1999) The life and work of Gustav Elfving. Stat Sci 14:174–193
53. Piesk T (2014) 4-cube t0.svg. In: Wikimedia Commons. https://commons.wikimedia.org/wiki/File:4-cube_t0.svg. Cited 27 June 2016
54. Quoirin M, Lepoivre P (1977) Improved media for in vitro culture of Prunus sp. Acta Hortic 78:437–442
55. Ross G (2012) Fisher and the millionaire: the statistician and the calculator. Significance 9:46–48
56. Ruen T (2011a) 9-cube t0.svg. In: Wikimedia Commons. https://commons.wikimedia.org/wiki/File:9-cube_t0.svg. Cited 27 June 2016
57. Ruen T (2011b) 10-cube t0.svg. In: Wikimedia Commons. https://commons.wikimedia.org/wiki/File:10-cube_t0.svg. Cited 27 June 2016
58. Salsburg D (2001) The lady tasting tea. W. H. Freeman and Co., New York
59. Schenk RU, Hildebrandt AC (1972) Medium and techniques for induction and growth of monocotyledonous and dicotyledonous plant cell cultures. Can J Bot 50:199–204
60. Schwarz A (2012) The becoming of the experimental mode. Scientiae Studia 10:65–83
61. Skoog F, Miller CO (1957) Chemical regulation of growth and organ formation in plant tissues cultured in vitro. Symp Soc Exp Biol 11:118–131
62. Smith DR, King KW, Williams MR (2015) What is causing the harmful algal blooms in Lake Erie? J Soil Water Conserv 70:27A–29A
63. Vacin EF, Went FW (1949) Some pH changes in nutrient solutions. Bot Gaz 110:605–613
64. White PR (1943) Nutrient deficiency studies and an improved inorganic nutrient for cultivation of excised tomato roots. Growth 7:53–65
65. Zappa F (1979) Packard Goose (song). On: Joe's Garage. Zappa Records, Los Angeles