Biomarkers from molecules to ecosystems and biobanks to genebanks

Conservation of Tropical Plant Species

Volumn 9781461437765, Issue , 2013, Pages 121-133

  Harding, Keith ^a   Benson, Erica E ^a  

^a Damar   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84879973893     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-3776-5_7     Document Type: Chapter

References (148)

1. Ahuja I, de Vos RCH, Bones AM, Hall RD (2010) Plant molecular stress responses face climate change. Trends Plant Sci 15: 664-674
2. Ayad WG, Hodgkin T, Jaradat A, Rao VR (1997) Molecular genetic techniques for plant genetic resources. Report of an IPGRI workshop, IPGRI, Rome, 9-11 Oct 1995
3. Balasubramanian R, Müller L, Kugler K, Hackl W, Pleyer L, Dehmer M, Graber A (2010) The impact of storage effects in biobanks on biomarker discovery in systems biology studies. Biomarkers 15: 677-683
4. Bank HL, Schmehl MK (1989) Parameters for evaluation of viability assays: Accuracy, precision, speci fi city, sensitivity, and standardization. Cryobiology 26: 203-211
5. Benson EE (1999) Plant conservation biotechnology. Taylor and Francis, London
6. Benson EE (2004) Cryo-conserving algal and plant diversity: historical perspectives and future challenges. In: Fuller B, Lane N, Benson EE (eds) Life in the frozen state. CRC Press, Florida
7. Benson EE (2008) Cryopreservation of phytodiversity: A critical appraisal of theory & practice. Crit Rev Plant Sci 27: 141-219
8. Benson EE, Harding K (2012) Cryopreservation of shoots and meristems: An overview of contemporary methodologies. In: Loyola-Vargas VM, Ocho-Alejo N (eds) Plant cell culture protocols, 3rd edn. Humana Press (in press
9. Benson EE, Krishnapillay B, Mansor M (1996) The potential of biotechnology in the in vitro conservation of Malaysian forest germplasm: An integrated approach. In: Hussein N, Bacon PS, Choon KK (eds) ODA proceedings of the 3rd conference forestry forest products research, vol 1 FRIM Publication, Kuala Lumpur
10. Benson EE, Betsou F, Amaral R, Santos LMA, Harding K (2011) Standard preanalytical codes: A new paradigm for environmental biobanking sectors explored in algal culture collections. Biopres Biobank 9: 1-12
11. Berjak P, Bartels P, Benson EE, Harding K, Mycock D, Pammenter N, Sershen, Wesley-Smith J (2011) Cryo-conservation of South African plant genetic diversity. In Vitro Cell Dev Biol Plant 47: 65-81
12. Betsou F, Lehmann S, Ashton G, Barnes M, Benson EE, Coppola D, DeSouza Y, Eliason J, Glazer B, Guadagni F, Harding K, Horsfall DJ, Kleeberger C, Nanni U, Prasad A, Shea K, Skubitz A, Somiari S, Gunter E (2010) Standard preanalytical coding for biospecimens: de fi ning the sample PREanalytical code. Cancer Epidemiol Biomarkers Prev 19: 1004-1011
13. Carpentier SC, Witters E, Laukens K, Van Onckelen H, Swennen R, Panis B (2007) Banana Musa spp. as a model to study the meristem proteome: Acclimation to osmotic stress. Proteomics 7: 92-105
14. Carpentier SC, Coemans B, Podevin N, Laukens K, Witters E, Matsumura H, Terauchi R, Swennen R, Panis B (2008) Functional genomics in a non-model crop: transcriptomics or proteomics? Physiol Plant 133 117-130
15. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794-12797
16. Chabot JR, Pedraza JM, Luitel P, Oudenaarden AV (2007) Stochastic gene expression out-ofsteady-state in the cyanobacterial circadian clock. Nature 450: 1249-1252
17. Coates DJ, Dixon KW (2007) Current perspectives of plant conservation biology. Aust J Bot 55: 187-193
18. Costa Nunes DA, Benson EE, Oltramari AC, Araujo PS, Moser JR, Viana AM (2003) In vitro conservation of Cedrela fi ssilis (Meliaceae) a native tree of the Brazilian Atlantic forest. Biodivers Conserv 12: 837-848
19. Côte FX, Goue O, Domergue R, Panis B, Jenny C (2000) In- field behaviour of banana plants ( Musa AA sp.) obtained after regeneration of cryopreserved embryonic cell suspensions. Cryo Lett 21: 19-24
20. Cramer W (2002) Biome models. In: Mooney HA, Canadell JG (eds) The earth system: biological and ecological dimensions of global environmental change, vol 2, Encyclopedia of global environmental change. Wiley, Chichester
21. de Vicente MC (2004) The evolving role of genebanks in the fast-developing field of molecular genetics. Issues in genetic resources. No. 11, IPGRI, Rome
22. de Vicente MC, Andersson MS (2006) DNA banks-providing novel options for genebanks? Topical reviews in agricultural biodiversity. IPGRI, Rome
23. Diekmann M, Putter CAJ (1996) FAO/IPGRI technical guidelines for the safe movement of germplasm. Musa , vol 15, 2nd edn. IPGRI, Rome
24. Donaldson JS, IUCN/SSC Cycad Specialist Group (2004) Cycads. Status survey and conservation action plan. IUCN, Gland
25. Fang JY, Wetten A, Johnston J (2008) Headspace volatile markers for sensitivity of cocoa ( Theobroma cacao L.) somatic embryos to cryopreservation. Plant Cell Rep 27: 453-461
26. Garming H, Roux N, Van den Houwe I (2010) The impact of the Musa international transit centre. Review of its services and cost-effectiveness and recommendations for rationalization of its operations. Bioversity International, Montpellier
27. Ghazoul J, Sheil D (2010) Tropical rain forest ecology, diversity, and conservation. Oxford University Press, New York
28. Gonzalez MA, Baraloto C, Engel J, Mori SA, Petronelli P, Riera B, Roger A, Thebaud C, Chave J (2009) Identi fi cation of Amazonian trees with DNA barcodes. PLoS One 4: e7483. doi: 10.1371/journal.pone.0007483
29. Harding K (1996) Approaches to assess the genetic stability of plants recovered from in vitro culture. In: Normah MN, Narimah MK, Clyde MM (eds) Proceedings of the international workshop: in vitro conservation of plant genetic resources. Plant Biotechnology Laboratory, University Kebangsaan Malaysia, Kuala Lumpur
30. Harding K (1999) Stability assessments of conserved plant germplasm. In: Benson EE (ed) Plant conservation biotechnology. Taylor and Francis, London
31. Harding K (2004) Genetic integrity of cryopreserved plant cells: A review. Cryo Lett 25: 3-22
32. Harding K (2010) Plant and algal cryopreservation: issues in genetic integrity, concepts in 'cryobionomics' and current applications in cryobiology. In: Proceedings of the Asia Paci fi c conference on plant tissues cultures and agrobiotechnology (APaCPa) 2007, Kuala Lumpur. Asia Pac J Mol Biol Biotech 18: 151-154
33. Harding K, Marzalina M, Krishnapillay B, Nashatul ZNA, Normah MN, Benson EE. (2000 Molecular stability assessments of trees regenerated from cryopreserved Mahogany seed germplasm using non-radioactive techniques to examine chromatin structure and DNA methylation status of the ribosomal genes. J Trop Forest Sci 12: 149-163
34. Harding K, Johnston J, Benson EE (2005) Plant and algal cell cryopreservation: issues in genetic integrity, concepts in 'Cryobionomics' and current European applications. In: Benett IJ, Bunn E, Clarke H, McComb JA (eds) Contributing to a sustainable future. Proceedings of the Australian branch of the IAPTC & B, Perth, Western Australia, pp 112-119
35. Harding K, Johnston JW, Benson EE (2009) Exploring the physiological basis of cryopreservation success and failure in clonally propagated in vitro crop plant germplasm. Agr Food Sci 18: 3-16
36. Higa TC, Paulilo MTS, Benson EE, Pedrotti E, Viana AM (2011) Developing seed cryobanking strategies for Tabebuia heptaphylla (Bignoniaceae) a hardwood tree of the Brazilian South Atlantic forest. Cryo Lett 32: 329-338
37. Holland NT, Smith MT, Eskenazi B, Bastaki M (2003) Biological sample collection and processing for molecular epidemiological studies. Mutat Res 543: 217-234
38. Holland NT, P fl eger L, Berger E, Ho A, Bastaki M (2005) Molecular epidemiology biomarkerssample collection and processing considerations. Toxicol Appl Pharmacol 206: 261-268
39. ISBER (2008) Best practices for repositories: collection, storage, retrieval and distribution of biological materials for research. Cell Preserv Technol 6: 3-58
40. Jackson WP, Kennedy K (2009) The global strategy for plant conservation: A challenge and opportunity for the international community. Trends Plant Sci 14: 578-580
41. Johnston JW, Harding K, Bremner DH, Souch G, Green J, Lynch PT, Grout B, Benson EE. (2005 HPLC analysis of plant DNA methylation: A study of critical methodological factors. Plant Physiol Bioch 43: 844-853
42. Johnston JW, Harding K, Benson EE (2007) Antioxidant status and genotypic tolerance of Ribes in vitro cultures to cryopreservation. Plant Sci 172: 524-534
43. Johnston J, Benson EE, Harding K (2009) Cryopreservation of in vitro Ribes shoots induces temporal changes in DNA methylation. Plant Physiol Bioch 47: 123-131
44. Johnston J, Pimbley I, Harding K, Benson EE (2010) Detection of 8-hydroxy-2 ¢ -deoxyguanosine a marker of DNA damage in germplasm and DNA exposed to cryogenic treatments. Cryo Lett 31: 1-13
45. Kaity A, Ashmore SE, Drew RA, Dulloo ME (2008) Assessment of genetic and epigenetic changes following cryopreservation in papaya. Plant Cell Rep 27: 1529-1539
46. Kaity A, Ashmore SE, Drew RA (2009) Field performance evaluation and genetic integrity assessment of cryopreserved papaya clones. Plant Cell Rep 28: 1421-1430
47. Karp A, Kresovich S, Bhat KV, Ayad WG, Hodgkin T (1997) Molecular tools in plant genetic resources conservation: A guide to the technologies. IPGRI Technical Bulletin, no. 2, IPGRI, Rome
48. Kosakivska IV (2008) Biomarkers of plants with different types of ecological strategies. Gen Appl Plant Physiol 34: 113-126
49. Kramer AT, Havens K (2009) Plant conservation genetics in a changing world. Trends Plant Sci 14: 599-607
50. Kranner I, Birtic S, Anderson KM, Pritchard HW (2006) Glutathione half-cell reduction potential: A universal stress marker and modulator of programmed cell death? Free Radical Biol Med 40: 2155-2165
51. Kugler KG, Hackl WO, Mueller LAJ, Fiegl H, Graber A, Pfeiffer RM (2011) The impact of sample storage time on estimates of association in biomarker discovery studies. J Clin Bioinform 1: 1-9
52. Laamanen J, Uosukainen M, Häggman H, Nukari A, Rantala S (2008) Cryopreservation of crop species in Europe. In: Proceedings of the CRYOPLANET COST action 871, Agrifood research working papers 153, MTT Agrifood Research, Oulu
53. Lakshmanan P, Reed BM, Sarasan V (2011) Special issue on biodiversity. In Vitro Cell Dev Biol Plant 47: 1-200
54. Leifert C, Cassells AC (2001) Microbial hazards in plant tissue and cell cultures. In Vitro Cell Dev Biol Plant 37: 133-138
55. Ahuja I, de Vos RCH, Bones AM, Hall RD (2010) Plant molecular stress responses face climate change. Trends Plant Sci 15: 664-674
56. Ayad WG, Hodgkin T, Jaradat A, Rao VR (1997) Molecular genetic techniques for plant genetic resources. Report of an IPGRI workshop, IPGRI, Rome, 9-11 Oct 1995
57. Balasubramanian R, Müller L, Kugler K, Hackl W, Pleyer L, Dehmer M, Graber A (2010) The impact of storage effects in biobanks on biomarker discovery in systems biology studies. Biomarkers 15: 677-683
58. Bank HL, Schmehl MK (1989) Parameters for evaluation of viability assays: Accuracy, precision, speci fi city, sensitivity, and standardization. Cryobiology 26: 203-211
59. Benson EE (1999) Plant conservation biotechnology. Taylor and Francis, London
60. Benson EE (2004) Cryo-conserving algal and plant diversity: historical perspectives and future challenges. In: Fuller B, Lane N, Benson EE (eds) Life in the frozen state. CRC Press, Florida
61. Benson EE (2008) Cryopreservation of phytodiversity: A critical appraisal of theory & practice. Crit Rev Plant Sci 27: 141-219
62. Benson EE, Harding K (2012) Cryopreservation of shoots and meristems: An overview of contemporary methodologies. In: Loyola-Vargas VM, Ocho-Alejo N (eds) Plant cell culture protocols, 3rd edn. Humana Press (in press
63. Benson EE, Krishnapillay B, Mansor M (1996) The potential of biotechnology in the in vitro conservation of Malaysian forest germplasm: An integrated approach. In: Hussein N, Bacon PS, Choon KK (eds) ODA proceedings of the 3rd conference forestry forest products research, vol I. FRIM Publication, Kuala Lumpur
64. Benson EE, Betsou F, Amaral R, Santos LMA, Harding K (2011) Standard preanalytical codes: A new paradigm for environmental biobanking sectors explored in algal culture collections. Biopres Biobank 9: 1-12
65. Berjak P, Bartels P, Benson EE, Harding K, Mycock D, Pammenter N, Sershen, Wesley-Smith J (2011) Cryo-conservation of South African plant genetic diversity. In Vitro Cell Dev Biol Plant 47: 65-81
66. Betsou F, Lehmann S, Ashton G, Barnes M, Benson EE, Coppola D, DeSouza Y, Eliason J, Glazer B, Guadagni F, Harding K, Horsfall DJ, Kleeberger C, Nanni U, Prasad A, Shea K, Skubitz A, Somiari S, Gunter E (2010) Standard preanalytical coding for biospecimens: de fi ning the sample PREanalytical code. Cancer Epidemiol Biomarkers Prev 19: 1004-1011
67. Carpentier SC, Witters E, Laukens K, Van Onckelen H, Swennen R, Panis B (2007) Banana Musa spp. as a model to study the meristem proteome: Acclimation to osmotic stress. Proteomics 7: 92-105
68. Carpentier SC, Coemans B, Podevin N, Laukens K, Witters E, Matsumura H, Terauchi R, Swennen R, Panis B (2008) Functional genomics in a non-model crop: transcriptomics or proteomics? Physiol Plant 133: 117-130
69. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794-12797
70. Chabot JR, Pedraza JM, Luitel P, Oudenaarden AV (2007) Stochastic gene expression out-ofsteady-state in the cyanobacterial circadian clock. Nature 450: 1249-1252
71. Coates DJ, Dixon KW (2007) Current perspectives of plant conservation biology. Aust J Bot 55: 187-193
72. Costa Nunes DA, Benson EE, Oltramari AC, Araujo PS, Moser JR, Viana AM (2003) In vitro conservation of Cedrela fi ssilis (Meliaceae) a native tree of the Brazilian Atlantic forest. Biodivers Conserv 12: 837-848
73. Côte FX, Goue O, Domergue R, Panis B, Jenny C (2000) In- field behaviour of banana plants ( Musa AA sp.) obtained after regeneration of cryopreserved embryonic cell suspensions. Cryo Lett 21: 19-24
74. Cramer W (2002) Biome models. In: Mooney HA, Canadell JG (eds) The earth system: biological and ecological dimensions of global environmental change, vol 2, Encyclopedia of global environmental change. Wiley, Chichester
75. de Vicente MC (2004) The evolving role of genebanks in the fast-developing field of molecular genetics. Issues in genetic resources. No. 11, IPGRI, Rome
76. De Vicente MC, Andersson MS (2006) DNA banks-providing novel options for genebanks? Topical reviews in agricultural biodiversity. IPGRI, Rome
77. Diekmann M, Putter CAJ (1996) FAO/IPGRI technical guidelines for the safe movement of germplasm. Musa , vol 15, 2nd edn. IPGRI, Rome
78. Donaldson JS, IUCN/SSC Cycad Specialist Group (2004) Cycads. Status survey and conservation action plan. IUCN, Gland
79. Fang JY, Wetten A, Johnston J (2008) Headspace volatile markers for sensitivity of cocoa ( Theobroma cacao L.) somatic embryos to cryopreservation. Plant Cell Rep 27: 453-461
80. Garming H, Roux N, Van den Houwe I (2010) The impact of the Musa international transit centre. Review of its services and cost-effectiveness and recommendations for rationalization of its operations. Bioversity International, Montpellier
81. Ghazoul J, Sheil D (2010) Tropical rain forest ecology, diversity, and conservation. Oxford University Press, New York
82. Gonzalez MA, Baraloto C, Engel J, Mori SA, Petronelli P, Riera B, Roger A, Thebaud C, Chave J (2009) Identi fi cation of Amazonian trees with DNA barcodes. PLoS One 4: e7483. doi: 10.1371/journal.pone.0007483
83. Harding K (1996) Approaches to assess the genetic stability of plants recovered from in vitro culture. In: Normah MN, Narimah MK, Clyde MM (eds) Proceedings of the international workshop: in vitro conservation of plant genetic resources. Plant Biotechnology Laboratory, University Kebangsaan Malaysia, Kuala Lumpur
84. Harding K (1999) Stability assessments of conserved plant germplasm. In: Benson EE (ed) Plant conservation biotechnology. Taylor and Francis, London
85. Harding K (2004) Genetic integrity of cryopreserved plant cells: A review. Cryo Lett 25: 3-22
86. Harding K (2010) Plant and algal cryopreservation: issues in genetic integrity, concepts in 'cryobionomics' and current applications in cryobiology. In: Proceedings of the Asia Paci fi c conference on plant tissues cultures and agrobiotechnology (APaCPa) 2007, Kuala Lumpur. Asia Pac J Mol Biol Biotech 18: 151-154
87. Harding K, Marzalina M, Krishnapillay B, Nashatul ZNA, Normah MN, Benson EE. (2000 Molecular stability assessments of trees regenerated from cryopreserved Mahogany seed germplasm using non-radioactive techniques to examine chromatin structure and DNA methylation status of the ribosomal genes. J Trop Forest Sci 12: 149-163
88. Harding K, Johnston J, Benson EE (2005) Plant and algal cell cryopreservation: issues in genetic integrity, concepts in 'Cryobionomics' and current European applications. In: Benett IJ, Bunn E, Clarke H, McComb JA (eds) Contributing to a sustainable future. Proceedings of the Australian branch of the IAPTC & B, Perth, Western Australia, pp 112-119
89. Harding K, Johnston JW, Benson EE (2009) Exploring the physiological basis of cryopreservation success and failure in clonally propagated in vitro crop plant germplasm. Agr Food Sci 18: 3-16
90. Higa TC, Paulilo MTS, Benson EE, Pedrotti E, Viana AM (2011) Developing seed cryobanking strategies for Tabebuia heptaphylla (Bignoniaceae) a hardwood tree of the Brazilian South Atlantic forest. Cryo Lett 32: 329-338
91. Holland NT, Smith MT, Eskenazi B, Bastaki M (2003) Biological sample collection and processing for molecular epidemiological studies. Mutat Res 543: 217-234
92. Holland NT, P fl eger L, Berger E, Ho A, Bastaki M (2005) Molecular epidemiology biomarkerssample collection and processing considerations. Toxicol Appl Pharmacol 206: 261-268
93. ISBER (2008) Best practices for repositories: collection, storage, retrieval and distribution of biological materials for research. Cell Preserv Technol 6: 3-58
94. Jackson WP, Kennedy K (2009) The global strategy for plant conservation: A challenge and opportunity for the international community. Trends Plant Sci 14: 578-580
95. Johnston JW, Harding K, Bremner DH, Souch G, Green J, Lynch PT, Grout B, Benson EE. (2005 HPLC analysis of plant DNA methylation: A study of critical methodological factors. Plant Physiol Bioch 43: 844-853
96. Johnston JW, Harding K, Benson EE (2007) Antioxidant status and genotypic tolerance of Ribes in vitro cultures to cryopreservation. Plant Sci 172: 524-534
97. Johnston J, Benson EE, Harding K (2009) Cryopreservation of in vitro Ribes shoots induces temporal changes in DNA methylation. Plant Physiol Bioch 47: 123-131
98. Johnston J, Pimbley I, Harding K, Benson EE (2010) Detection of 8-hydroxy-2 ¢ -deoxyguanosine a marker of DNA damage in germplasm and DNA exposed to cryogenic treatments. Cryo Lett 31: 1-13
99. Kaity A, Ashmore SE, Drew RA, Dulloo ME (2008) Assessment of genetic and epigenetic changes following cryopreservation in papaya. Plant Cell Rep 27: 1529-1539
100. Kaity A, Ashmore SE, Drew RA (2009) Field performance evaluation and genetic integrity assessment of cryopreserved papaya clones. Plant Cell Rep 28: 1421-1430
101. Karp A, Kresovich S, Bhat KV, Ayad WG, Hodgkin T (1997) Molecular tools in plant genetic resources conservation: A guide to the technologies. IPGRI Technical Bulletin, no. 2, IPGRI, Rome
102. Kosakivska IV (2008) Biomarkers of plants with different types of ecological strategies. Gen Appl Plant Physiol 34: 113-126
103. Kramer AT, Havens K (2009) Plant conservation genetics in a changing world. Trends Plant Sci 14: 599-607
104. Kranner I, Birtic S, Anderson KM, Pritchard HW (2006) Glutathione half-cell reduction potential: A universal stress marker and modulator of programmed cell death? Free Radical Biol Med 40: 2155-2165
105. Kugler KG, Hackl WO, Mueller LAJ, Fiegl H, Graber A, Pfeiffer RM (2011) The impact of sample storage time on estimates of association in biomarker discovery studies. J Clin Bioinform 1: 1-9
106. Laamanen J, Uosukainen M, Häggman H, Nukari A, Rantala S (2008) Cryopreservation of crop species in Europe. In: Proceedings of the CRYOPLANET COST action 871, Agrifood research working papers 153, MTT Agrifood Research, Oulu
107. Lakshmanan P, Reed BM, Sarasan V (2011) Special issue on biodiversity. In Vitro Cell Dev Biol Plant 47: 1-200
108. Leifert C, Cassells AC (2001) Microbial hazards in plant tissue and cell cultures. In Vitro Cell Dev Biol Plant 37: 133-138
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