Use of Video Bioinformatics Tools in Stem Cell Toxicology

Handbook of Nanotoxicology, Nanomedicine and Stem Cell Use in Toxicology

Volumn , Issue , 2014, Pages 379-402

  Talbot, Prue ^a   Zur Nieden, Nicole I ^a   Lin, Sabrina ^a   Martinez, Ivann ^a   Guan, Ben ^b   Bhanu, Bir ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Riverside   (United States)

Author keywords

Cigarette smoke toxicity; Live cell imaging; Prenatal model; Stem cells; Toxicology; Video bioinformatics

Indexed keywords

BIOINFORMATICS; CYTOLOGY; DATA ACQUISITION; OSTEOBLASTS; TOXICITY; VIDEO RECORDING;

BIOINFORMATICS TOOLS; CIGARETTE SMOKE TOXICITIES; ENVIRONMENTAL TOXICANTS; FUTURE IMPROVEMENTS; HUMAN EMBRYONIC STEM CELLS; LIVE-CELL IMAGING; PROTOCOL DEVELOPMENT; TOXICOLOGY;

STEM CELLS;

EID: 84940845496     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118856017.ch21     Document Type: Chapter

References (85)

1. Adler S, Pellizzer C, Hareng L, Hartung T, Bremer S. 2008. First steps in establishing a developmental toxicity test method based on human embryonic stem cells. Toxicol. In Vitro 22(1): 200-211.
2. Alworth SV,Watanabe H, Lee JS. 2010. Teachable, high-content analytics for live-cell, phase contrast movies. J. Biomol. Screen. 15(8): 968-977, 1087057110373546 [pii]. doi:10.1177/1087057110373546.
3. Amit M, Itskovitz-Eldor J. 2002. Derivation and spontaneous differentiation of human embryonic stem cells. J. Anat. 200(Pt 3): 225-232.
4. Bahl V, Lin S, Xu N, Davis B, Wang YH, Talbot P. 2012. Comparison of electronic cigarette refill fluid cytotoxicity using embryonic and adult models. Reprod. Toxicol. 34(4): 529-537, S0890-6238(12)00283-3 [pii]. doi:10.1016/j.reprotox.2012.08.001.
5. Bailey J. 2005. Non-human primates in medical research and drug development: a critical review. Biogenic Amines 19(4-6): 235-255.
6. Barouki R, Gluckman PD, Grandjean P, Hanson M, Heindel JJ. 2012. Developmental origins of non-communicable disease: implications for research and public health. Environ. Health 11: 42, 1476-069X-11-42 [pii].
7. Basma H, Soto-Gutiérrez A, Yannam GR, Liu L, Ito R, Yamamoto T, Ellis E, Carson SD, Sato S, Chen Y, Muirhead D, Navarro-Álvarez N, Wong RJ, Roy-Chowdhury J, Platt JL, Mercer DF, Miller JD, Strom SC, Kobayashi N, Fox IJ. 2009. Differentiation and transplantation of human embryonic stem cell-derived hepatocytes. Gastroenterology 136(3): 990-999. doi:10.1053/j.gastro.2008.10.047.
8. Behar RZ, Bahl V, Wang Y, Weng J-H, Lin S, Talbot P. 2012a. Adapting the MTT cytotoxicity assay for use with mouse neuronal stem cells and human embryonic stem cells. Curr. Protoc. Stem Cell Biol. 23: 1C.13.1-1C.13.21.
9. Behar R, Bahl V,Wang Y, Lin S, Xu N, Davis B, Talbot P. 2012b. A method for rapid dose-response screening of environmental chemicals using human embryonic stem cells. J. Pharmacol. Toxicol. Methods 66(3): 238-245, S1056-8719(12)00076-7 [pii]. doi:10.1016/j.vascn.2012.07.003.
10. Cervinka M, Cervinkova Z, Rudolf E. 2008. The role of time-lapse fluorescent microscopy in the characterization of toxic effects in cell populations cultivated in vitro. Toxicol. In Vitro 22(5): 1382-1386, S0887-2333(08)00082-9 [pii]. doi:10.1016/j.tiv.2008.03.011.
11. Cuthbertson RA, Beck F. 1990. Postimplantation whole embryo culture: a new method for studying ocular development. Invest. Ophthalmol. Vis. Sci. 31(8): 1653-1656.
12. Dechanet C, Anahory T, Mathieu Daude JC, Quantin X, Reyftmann L, Hamamah S, Hedon B, Dechaud H. 2011. Effects of cigarette smoking on reproduction. Hum. Reprod. Update 17(1): 76-95, dmq033 [pii]. doi:10.1093/humupd/dmq033.
13. Ek M, Söderdahl T, Küppers-Munther B, Edsbagge J, Andersson TB, Björquist P, Cotgreave I, Jernströmb B, Ingelman-Sundberg M, Johansson I. 2007. Expression of drug metabolizing enzymes in hepatocyte-like cells derived from human embryonic stem cells. Biochem. Pharmacol. 74: 496-503.
14. EPA. 1992. EPA Report/600/6-90/006F: Respiratory Health Effects of Passive Smoking: Lung Cancer and Other Disorders, Washington, DC.
15. Festag M, Sehner C, Steinberg P, Viertel B. 2007a. An in vitro embryotoxicity assay based on the disturbance of the differentiation of murine embryonic stem cells into endothelial cells. I: establishment of the differentiation protocol. Toxicol. In Vitro 21(8): 1619-1630.
16. Festag M, Viertel B, Steinberg P, Sehner C. 2007b. An in vitro embryotoxicity assay based on the disturbance of the differentiation of murine embryonic stem cells into endothelial cells. II. Testing of compounds. Toxicol. In Vitro 21(8): 1631-1640.
17. Gartner C, Hall W. 2010. Harm reduction policies for tobacco users. Int. J. Drug Policy 21(2): 129-130, S0955-3959(09) 00134-0 [pii]. doi:10.1016/j.drugpo.2009.10.008.
18. Genschow E, Spielmann H, Scholz G, Pohl I, Seiler A, Clemann N, Bremer S, Becker K. 2004. Validation of the embryonic stem cell test in the international ECVAM validation study on three in vitro embryotoxicity tests. Altern. Lab. Anim. 32(3): 209-244.
19. Gieseke C, Talbot P. 2005. Cigarette smoke inhibits hamster oocyte pickup by increasing adhesion between the oocyte cumulus complex and oviductal cilia. Biol. Reprod. 73(3): 443-451.
20. Grandjean P, Bellinger D, Bergman A, Cordier S, Davey-Smith G, Eskenazi B, Gee D, Gray K, Hanson M, van den Hazel P, Heindel JJ, Heinzow B, Hertz-Picciotto I, Hu H, Huang TT, Jensen TK, Landrigan PJ, McMillen IC, Murata K, Ritz B, Schoeters G, Skakkebaek NE, Skerfving S,Weihe P. 2007. The faroes statement: human health effects of developmental exposure to chemicals in our environment. Basic Clin. Pharmacol. Toxicol. 102: 73-75.
21. Guan X, Bhanu B, Thakoor N, Talbot P, Lin S. 2011. Human embryonic stem cell detection by spatial information and mixture of Gaussians. IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology, July 27-29, 2011, San Jose, CA.
22. Guan X, Bhanu B, Talbot P, Lin S. 2012a. Detection of non-dynamic blebbing single unattached human embryonic stem cell. International Conference on Image Processing, Sept 30-Oct 3, 2012, Orlando, FL.
23. Guan X, Bhanu B, Talbot P, Lin S. 2012b. Automatic human embryonic stem cell detection. 2nd Annual IEEE Healthcare Informatics, Imaging, and Systems Biology Conference, September 27-28, 2012, San Diego.
24. Guan BX, Bhanu B, Thakoor N, Talbot P, and Lin S. 2013. Automatic cell region detection by K-means with weighted entropy. International Symposium on Biomedical Imaging, April.
25. Guengerich FP. 2011. Mechanisms of drug toxicity and relevance to pharmaceutical development. Drug Metab. Pharmacokinet. 26: 3-14.
26. Hatsukami DK, Lemmonds C, Zhang Y, Murphy SE, Le C, Carmella SG, Hecht SS. 2004. Evaluation of carcinogen exposure in people who used "reduced exposure" tobacco products. J. Natl. Cancer Inst. 96(11): 844-852.
27. Hatsukami DK, Joseph AM, Lesage M, Jensen J, Murphy SE, Pentel PR, Kotlyar M, Borgida E, Le C, Hecht SS. 2007. Developing the science base for reducing tobacco harm. Nicotine Tob. Res. 9(Suppl 4): S537-S553, 788242874 [pii]. doi:10.1080/14622200701679040.
28. Ho PJ, Yen ML, Yet SF, Yen BL. 2012. Current applications of human pluripotent stem cells: possibilities and challenges. Cell Transplant. 21(5): 801-814, ct0431ho [pii]. doi:10.3727/096368911X627507.
29. Hua M, Yip H, Talbot P. 2011. Mining data on usage of electronic nicotine delivery systems (ENDS) from YouTube videos. Tob. Control . doi:10.1136/tobaccocontrol-2011-050226.
30. Inoue S. 1987. Video microscopy of living cells and dynamic molecular assemblies. Appl. Optic 26(16): 3219-3225. doi:10.1364/AO.26.003219.
31. Inoue S. 1988. Progress in video microscopy. Cell Motility Cytoskel. 10(1-2): 13-17. doi:10.1002/cm.970100105.
32. Kang, K. S., and Trosko, J. E. (2011). Stem cells in toxicology: fundamental biology and practical considerations. Toxicol. Sci. 120 Suppl 1, S269-S289, kfq370 [pii] 10.1093/toxsci/kfq370, 10.1186/1476-069X-11-42.
33. Knoll M, Talbot P. 1998. Cigarette smoke inhibits oocyte cumulus complex pick-up by the oviduct independent of ciliary beat frequency. Reprod. Toxicol. 12: 57-68.
34. Liang CC, Park AY, Guan JL. 2007. In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro. Nat. Protoc. 2(2): 329-333. doi:10.1038/nprot.2007.30.
35. Lin S, Talbot P. 2011. Methods for culturing mouse and human embryonic stem cells. Methods Mol. Biol. 690: 31-56. doi:10.1007/978-1-60761-962-8_2.
36. Lin S, Tran V, Talbot P. 2009. Comparison of toxicity of smoke from traditional and harm reduction cigarettes using embryonic stem cells as a novel model for pre-implantation development. Hum. Reprod. 24: 386-397.
37. Lin S, Fonteno S, Weng JH, Talbot P. 2010a. Comparison of the toxicity of smoke from conventional and harm reduction cigarettes using human embryonic stem cells. Toxicol. Sci. 118(1): 202-212, kfq241 [pii]. doi:10.1093/toxsci/kfq241.
38. Lin S, Fonteno S, Satish S, Bhanu B, Talbot P. 2010b. Video bioinformatics analysis of human embryonic stem cell colony growth. J. Visual. Exp. 39: 1933.
39. Ludwig T, Thomson JA. 2007. Defined, feeder-independent medium for human embryonic stem cell culture. Curr. Protoc. Stem Cell Biol., Chapter 1, Unit 1C 2 .
40. Martin GR. 1981. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. U. S. A. 78(12): 7634-7638.
41. Mouche I, Malesic L, Gillardeaux O. 2011. FETAX assay for evaluation of developmental toxicity. Methods Mol. Biol. 691: 257-269.
42. Nalos L, Varkevisser R, Jonsson MK, Houtman MJ, Beekman JD, van der Nagel R, Thomsen MB, Duker G, Sartipy P, de Boer TP, Peschar M, Rook MB, van Veen TA, van der Heyden MA, Vos MA. 2012. Comparison of the IKr blockers moxifloxacin, dofetilide and E-4031 in five screening models of pro-arrhythmia reveals lack of specificity of isolated cardiomyocytes. Br. J. Pharmacol. 165(2): 467-478.
43. Nichols J, Smith A. 2009. Naive and primed pluripotent states. Cell Stem Cell 4(6): 487-492, S1934-5909(09)00224-0 [pii]. doi:10.1016/j.stem.2009.05.015.
44. Nichols J, Smith A. 2011. The origin and identity of embryonic stem cells. Development 138(1): 3-8, 138/1/3 [pii]. doi:10.1242/dev.050831.
45. zur Nieden NI, Baumgartner L. 2010. Assessing developmental osteotoxicity of chlorides in the embryonic stem cell test. Reprod. Toxicol. 30(2): 277-283.
46. zur Nieden NI, Ruf LJ, Kempka G, Hildebrand H, Ahr HJ. 2001. Molecular markers in embryonic stem cells. Toxicol. In Vitro 15(4-5): 455-461.
47. zur Nieden NI, Kempka G, Ahr HJ. 2003. In vitro differentiation of embryonic stem cells into mineralized osteoblasts. Differentiation 71(1): 18-27.
48. zur Nieden NI,Kempka G, Ahr HJ. 2004. Molecular multiple endpoint embryonic stem cell test-a possible approach to test for the teratogenic potential of compounds. Toxicol. Appl. Pharmacol. 194(3): 257-269.
49. zur Nieden NI, Kempka G, Rancourt DE, Ahr HJ. 2005. Induction of chondro-, osteo-and adipogenesis in embryonic stem cells by bone morphogenetic protein-2: effect of cofactors on differentiating lineages. BMC Dev. Biol. 5: 1.
50. zur Nieden NI, Price FD, Davis LA, Everitt RE, Rancourt DE. 2007. Gene profiling on mixed embryonic stem cell populations reveals a biphasic role for beta-catenin in osteogenic differentiation. Mol. Endocrinol. 21(3): 674-685.
51. zur Nieden NI, Davis LA, Rancourt DE. 2010a. Comparing three novel endpoints for developmental osteotoxicity in the embryonic stem cell test. Toxicol. Appl. Pharmacol. 247(2): 91-97.
52. zur Nieden NI, Davis LA, Rancourt DE. 2010b. Monolayer cultivation of osteoprogenitors shortens duration of the embryonic stem cell test while reliably predicting developmental osteotoxicity. Toxicology 277(1-3): 66-73.
53. Okabe S, Forsberg-Nilsson K, Spiro AC, Segal M, McKay RD. 1996. Development of neuronal precursor cells and functional postmitotic neurons from embryonic stem cells in vitro. Mech. Dev. 59(1): 89-102.
54. Parvin B, Yang Q, Fontenay G, Barcellos-Hoff MH. 2003. An imaging bioinformatics system for phenotypic analysis. IEEE Trans. SMC B 33(5): 814-824.
55. Phillips BW, Belmonte N, Vernochet C, Ailhaud G, Dani C. 2001. Compactin enhances osteogenesis in murine embryonic stem cells. Biochem. Biophys. Res. Commun. 284(2): 478-484.
56. Pointon A, Abi-Gerges N, Cross MJ, Sidaway JE. 2013. Phenotypic profiling of structural cardiotoxins in vitro reveals dependency on multiple mechanisms of toxicity. Toxicol. Sci. 132(2): 317-326.
57. Prelog M. 2011. Smoking and reproduction. In Cigarette Smoke Toxicity: Linking Individual Chemcials to Human Disease, Bernhard D (ed).Wiley-VCH Verlag GmbH & Co.:Weinheim.
58. Pust S, Dyve AB, Torgersen ML, van Deurs B, Sandvig K. 2010. Interplay between toxin transport and flotillin localization. PLoS One 5(1): e8844. doi:10.1371/journal.pone.0008844.
59. Reubinoff BE, Pera MF, Fong CY, Trounson A, Bongso A. 2000. Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol. 18(4): 399-404.
60. Riveles K, Tran V, Roza R, Kwan D, Talbot P. 2007. Smoke from traditional commercial, harm reduction and research brand cigarettes impairs oviductal functioning in hamsters (Mesocricetus auratus) in vitro. Hum. Reprod. 22(2): 346-355.
61. Rodriguez LG, Wu X, Guan JL. 2005. Wound-healing assay. Methods Mol. Biol. 294: 23-29.
62. Rudolf E, Cervinka M. 2010. Zinc pyrithione induces cellular stress signaling and apoptosis in Hep-2 cervical tumor cells: the role of mitochondria and lysosomes. Biometals 23(2): 339-354. doi:10.1007/s10534-010-9302-8.
63. San Miguel SM, Opperman LA, Allen EP, Zielinski J, Svoboda KK. 2010. Antioxidants counteract nicotine and promote migration via RacGTP in oral fibroblast cells. J. Periodontol. 81(11): 1675-1690. doi:10.1902/jop.2010.100187.
64. Schick S, Glantz S. 2005. Philip Morris toxicological experiments with fresh sidestream smoke: more toxic than mainstream smoke. Tob. Control 14(6): 396-404, 14/6/396 [pii]. doi:10.1136/tc.2005.011288.
65. Scholz G, Genschow E, Pohl I, Bremer S, Paparella M, Raabe H, Southee J, Spielmann H. 1999. Prevalidation of the embryonic stem cell test (EST)-a new in vitro embryotoxicity test. Toxicol. In Vitro 13(4-5): 675-681.
66. Schuster D, Laggner C, Langer T. 2005. Why drugs fail-a study on side effects in new chemical entities. Curr. Pharm. Des. 11: 3545-3559.
67. Seiler A, Visan A, Buesen R, Genschow E, Spielmann H. 2004. Improvement of an in vitro stem cell assay for developmental toxicity: the use of molecular endpoints in the embryonic stem cell test. Reprod. Toxicol. 18(2): 231-240.
68. Shah RR. 2006. Can pharmacogenetics help rescue drugs withdrawn from the market? Pharmacogenomics 7: 889-908.
69. Shields PG. 2002. Tobacco smoking, harm reduction, and biomarkers. J. Natl. Cancer Inst. 94(19): 1435-1444.
70. Spielmann H, Pohl I, Döring B, Liebsch M, Moldenhauer F. 1997. The embryonic stem cell test (EST), an in vitro embryotoxicity test using two permanent mouse cell lines: 3T3 fibroblasts and embryonic stem cells. In Vitro Toxicol. 10: 119-127.
71. Stephens DJ, Allan VJ. 2003. Light microscopy techniques for live cell imaging. Science 300(5616): 82-86. doi:10.1126/science.1082160, 300/5616/82 [pii].
72. Swedlow JR, Platani M. 2002. Live cell imaging using wide-field microscopy and deconvolution. Cell Struct. Funct. 27(5): 335-341.
73. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S. 2007. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131(5): 861-872, S0092-8674(07)01471-7 [pii]. doi:10.1016/j.cell.2007.11.019.
74. Talbot P. 2008. In vitro assessment of reproductive toxicity of tobacco smoke and its constituents. Birth Defects Res. C Embryo Today 84(1): 61-72.
75. Talbot P, Lin S. 2011a. Cigarette smoke's effect on fertilization and pre-implantation development: assessment using animal models, clinical data, and stem cells. J. Biol. Res. 44: 189-194.
76. Talbot P, Lin S. 2011b. Mouse and human embryonic stem cells: can they improve human health by preventing disease? Curr. Top. Med. Chem. 11(13): 1638-1652.
77. Thomson JA, Kalishman J, Golos TG, Durning M, Harris CP, Becker RA, Hearn JP. 1995. Isolation of a primate embryonic stem cell line. Proc. Natl. Acad. Sci. U. S. A. 92(17): 7844-7848.
78. Thomson JA, Kalishman J, Golos TG, Durning M, Harris CP, Hearn JP. 1996. Pluripotent cell lines derived from common marmoset (Callithrix jacchus) blastocysts. Biol. Reprod. 55(2): 254-259.
79. Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, Jones JM. 1998. Embryonic stem cell lines derived from human blastocysts. Science 282(5391): 1145-1147.
80. Trtchounian A, Talbot P. 2010. Electronic nicotine delivery systems-is there a need for regulation? Tob. Control 20: 47-52.
81. Trtchounian A, Willams M, Talbot P. 2010. Conventional and electronic cigarettes (E-cigarettes) have different smoking properties. Nicotine Tob. Res. 12(9): 905-912.
82. Warner KE. 2005. Will the next generation of "safer" cigarettes be safer? J. Pediatr. Hematol. Oncol. 27(10): 543-550.
83. Williams M, Talbot P. 2011. Variability among electronic cigarettes in the pressure drop, airflow rate, and aerosol production. Nicotine Tob. Res. 13(12): 1276-1283. doi:10.1093/ntr/ntr164.
84. Wollert T, Langford GM. 2009. High resolution multimode light microscopy of cell migration: long-term imaging and analysis. Methods Mol. Biol. 586: 3-21. doi:10.1007/978-1-60761-376-3_1.
85. Zeller M, Hatsukami D, Backinger C, Benowitz N, Biener L, Burns D, Clark P, Connolly G, Djordjevic MV, Eissenberg T, Giovino GA, Healton C, Hecht SS, Henningfield JE, Husten C, Kobus K, Leischow S, Levy DT, Marcus S, Myers ML, Parascandola M, Ponkshe P, Shields PG, Slovic P, Sweanor D, Warner KE. 2009. The strategic dialogue on tobacco harm reduction: a vision and blueprint for action in the United States. Tob. Control 18(4): 324-332.