Abstract
The procedure for the successful extraction of nucleic acids depends on the type of sample being extracted and the purpose of the extraction. Protocols for the extraction of high copy number DNA samples vary significantly from those of degraded DNA samples. This study involved the development of a DNA extraction protocol that includes a cleaning procedure designed to remove external contaminants (e.g. biological, environmental, or chemical). This protocol, used to test ancient human bones, was used for testing ancient and degraded DNA samples from sturgeons.
We analysed three specimens captured in the Guadalquivir River from the mid-1970s to the early 1980s (preserved at the Biological Station of Doñana in Seville [EBD], Spain), and also included one from the Ebro river (stored at the Botanical Institute of Barcelona), and one from the collections at the Department of Zoology at the Science Faculty of the University of Granada (UGP).
The sturgeon samples were processed with forensic scientific techniques. In forensic sciences, the external components of a sample must be cleaned to ensure the results are from the specimen being tested rather than the contaminants from handling the specimens or external exposure. The samples were cleaned to remove potential contaminants and subjected to an organic extraction procedure.
A cleaning procedure was selected to obtain the individual sturgeon DNA and the samples were sufficiently cleaned and the contaminants removed from the sample. This extraction ensures reliable amplification and cloning.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adegoke JA, Ighavini BO, Onuigbo RO. 1991. Characteristic features of the sonicated DNA of Agama agama L. (Reptilia, Agamidae) on hydroxyapatite columns, using mouse DNA as a reference. Genetica 83: 171–180.
Anderson TD, Ross JP, Roby RK, Lee DA, Holland MM. 1999. A validation study for the extraction and analysis of DNA from human nail material and its application to forensic casework. J. Forensic Sci. 44(5): 1053–1056.
Bender K, Farfán MJ, Schneider PM. 2004. Preparing of degrades human DNA under controlled conditions. Forensic Sci. Int. 139: 135–140.
Butler JM. 2005. Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers, 2nd edn. Elsevier Academic, New York, pp. 145–180.
Cano RJ. 1996. Analysing ancient DNA. Endeavour 20(4): 162–167.
Capelli C, Tschentscher F, Pascali VL. 2003. ‘Ancient’ protocols for the crime scene? Similarities and differences between forensic genetics and ancient DNA analysis. Forensic Sci. Int. 131: 59–64.
Capello FB. 1869. Catalogo dos peixes do Portugal que existem no Museu de Lisboa. J. Sci. Math. Phys. Nat. 2: 131–193.
Carracedo A, Bär W, Lincoln P, Mayr W, Morling N, Olaisen B, Schneider P, Budowle B, Brinkmann B, Gill P, Holland M, Tully G, Wilson M. 2000. DNA commission of the international society for forensic genetics: guidelines for mitochondrial DNA typing. Forensic Sci. Int. 110(2): 79–85; Int. J. Legal Med. 113(4): 193–196; Vox Sang. 79(2): 121–125.
Comey CT, Koons BW, Presley KW, Smerick JV, Sobieralski CA, Stanley DM and Baechtel FS. 1994. DNA extraction strategies for amplified fragment length polymorphism analysis. J. Forensic Sci. 39: 1254–1269.
de la Herrán R, Robles F, Martínez-Espín E, Lorente JA, Ruiz Rejón C, Garrido-Ramos MA, Ruiz Rejón M. 2004. Genetic identification of western Mediterranean sturgeons and its implication for conservation. Conserv. Genet. 5: 545–551.
Donoghue MJ, Doyle JA, Gauthier J, Kluge AG, Rowe T. 1989. The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20: 431–460.
Eglinton G, Logan GA. 1991. Molecular preservation. Phil. Trans. R. Soc. London Ser. 333: 315–328
Findlay I, Frazier R, Taylor A, Urquhart A. 1997. Single cell DNA fingerprinting for forensic applications. Nature 389: 555–556.
Garrido-Ramos MA, Soriguer MC, de la Herrán R, Jamilena M, Ruiz Rejón C, Domezain A, Hernando JA, Ruiz Rejón M. 1997. Morphometric and genetic analysis as proof of the existence of two sturgeon species in the Guadalquivir River. Mar. Biol. 129: 33–39.
Gill P. 1997. The utility of ‘substrate controls’ in relation to ‘contamination’. Forensic Sci. Int. 85: 105–111.
Gill P, Whitaker J, Flaxman C, Brown N, Buckleton J. 2000. An investigation of the rigor of interpretation rules for STRs derived from less than 100pg of DNA. Forensic Sci. Int. 112: 17–40.
Gonçalves BC. 1942. Colecção oceanográfica de D. Carlos I. Peixes. Trav. Stn. Biol. Marit. Lisb. 46: 1–108.
Handt O, Höss M, Krings M, Pääbo S. 1994. Ancient DNA: methodological challenges. Experientia 50: 524–529.
Jobling MA, Hurles ME, Tyler-Smith C. 2004. Human Evolutionary Genetics Origins, Peoples and Disease. Garland Publishing, New York, pp. 473–478.
Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362: 709–715.
Lygo JE, Jhonson PE, Holdaway DJ, Woodroffe S, Whitaker JP, Clayton TM, Kimpton CP, Gill P. 1994. The validation of short tandem repeat (STR) loci for use in forensic casework. Int. J. Legal Med. 107(2): 77–89.
McDowall RM. 1999. Different kinds of diadromy: different kinds of conservation problems. ICES J. Mar. Sci. 56(4): 410–412.
Moran N, Munson MA, Baumann P, Ishikawa H. 1993. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc. R. Soc. London Ser. B. 253: 167–171.
Moreira D. 1998. Efficient removal of PCR inhibitors using agarose embedded DNA preparations. Nucleic Acids Res. 26: 3309–3310.
Ochman H, Wilson AW. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26: 74–86.
Pääbo S, Poinar H, Serre D, Jaenicke-Després V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. 2004. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38: 645–679.
Robles F, de la Herrán R, Ludwig A, Ruiz Rejon C, Ruiz Rejon M, Garrido-Ramos MA. 2004. Evolution of ancient satellite DNAs in sturgeon genomes. Gene 338(1): 133–142.
Robles F, de la Herrán R, Ludwig A, Ruiz Rejon C, Ruiz Rejon M, Garrido-Ramos MA. 2005. Genomic organization and evolution of the 5s ribosomal DNA in the ancient fish sturgeon. Genome 48(1): 18–28.
Rys PN, Persing DH. 1993. Preventing false positives: quantitative evaluation of three protocols for inactivation of polymerase chain reaction amplification products. J. Clin. Microbiol. 31: 2356–2360.
Svetovidov AN. 1989. Acipenseridae. In: Fishes of North-eastern Atlantic and Mediterranean, Whitehead PJP, Bauchot ML, Tortonese E (eds.), 2nd edn. UNESCO, Paris, pp. 220–225.
Vaneechoutte M, Van Eldere J. 1997. The possibilities and limitations of nucleic acid amplification technology in diagnostic microbiology. J. Med. Microbiol. 46: 188–194.
van Oorschot RAH, Jones MJ. 1997. DNA fingerprints from fingerprints. Nature 387: 767.
Varricchio D. 1993. Bone microstructure of the Upper Cretaceous dinosaur Troodon formosus. J. Vert. Paleontol. 113: 99–104.
Wilson IG. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63(10): 3741–3751.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science + Business Media B.V
About this chapter
Cite this chapter
Martinez-Espin, E., Martinez-Gonzalez, L.J., Alvarez, J.C., Roby, R.K., Lorente, J.A. (2009). Forensic Strategies Used for DNA Extraction of Ancient and Degraded Museum Sturgeon Specimens. In: Carmona, R., Domezain, A., García-Gallego, M., Hernando, J.A., Rodríguez, F., Ruiz-Rejón, M. (eds) Biology, Conservation and Sustainable Development of Sturgeons. Fish & Fisheries Series, vol 29. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8437-9_5
Download citation
DOI: https://doi.org/10.1007/978-1-4020-8437-9_5
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-8436-2
Online ISBN: 978-1-4020-8437-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)