Real-Time Polymerase Chain Reaction For Detection Of Optimal Thermal Profile For DNA Templates From Air-Dried Insect Collection Material

Kokina, Inese; Barševskis, Arvīds; Latvele, Rita; Aksjuta, Kristīna; Jahundoviča, Inese

doi:10.1515/prolas-2015-0003

Abstract

The thermal profile for polymerase chain reaction (PCR) technique is the main concern in obtaining the PCR product. Determination of optimal thermal profile can be achieved by various techniques, the main objectives of which are simplicity and cost effectiveness of the method. Real-time PCR is a novel molecular biology method widely used in different fields, recognised by its accuracy and precision. In the present work, the thermal profile was estimated for DNA from air-dried collection material of Notiophilus genus and new sequences were obtained for Gene-Bank. Air-dried entomological collections exist around the world and the use of DNA from such type of material is widespread and offers various unique preferences. The purpose of the study was to assess the suitability of different primer annealing temperatures (42 °C – 55 °C) for universal mitochondrial DNA COI gene primer pair HCO/LCO using real-time PCR method. During this study we demonstrate that real-time PCR could be useful to determine the optimal thermal profile for low-yield DNA for increasing the number of qualitative DNA sequences.

References

Alroy, J. (2003). Taxonomic inflation and body mass distributions in North American fossil mammals. J. Mammal.,84, 431–443.10.1644/1545-1542(2003)084<;0431:TIABMD>2.0.CO;2
Search in Google Scholar
Alvarez, M. J., Vila-Ortiz, G. J., Salibe, M. C., Podhajcer, O. L., Pitossi, F. J. (2007). Model based analysis of real-time PCR data from DNA binding dye protocols. BioMed Central Bioinformatics,8, 85–95.10.1186/1471-2105-8-85
Search in Google Scholar
Barševskis, A. (2003). Latvijas skrejvaboles (Coleoptera: Carabidae, Trachypachidae & Rhysodidae) [Ground beetles (Coleoptera: Carabidae, Trachypachidae & Rhysodidae) of Latvia]. Daugavpils: Baltic Institute of Coleopterology. 264 lpp. (in Latvian).
Search in Google Scholar
Barševskis, A. (2007). Biogeography of the genus Notiophilus Dumeril, 1806 (Coleoptera: Carabidae). Baltic J. Coleopterol., 7 (1), 121–135.
Search in Google Scholar
Burns, M. J., Nixon, G. J., Foy, C. A., Harris, N. (2005). Standardisation of data from real-time quantitative PCR methods — evaluation of outliers and comparison. BioMed Central Biotechnol., 5, 31–44.10.1186/1472-6750-5-31
Search in Google Scholar
Bustin, S. A., Benes, V., Nolan, T., Pfaffl, M. W. (2005). J. Mol. Endocrinol.34, 597–601.10.1677/jme.1.01755
Search in Google Scholar
Calderon-Cortes, N., Quesada, M., Cano-Camacho, H., Zavala-Paramo, G. (2010). A simple and rapid method for DNA isolation from Xylophagus insects. Int. J. Mol. Sci., 11, 5056–5064.10.3390/ijms11125056
Search in Google Scholar
Dahlgren, T. G., Lundberg, J., Pleijel, F., Sundberg, P. (2000). Morphological and molecular evidence of the phylogeny of Nereidiform polychaetes (Annelida). J. Zool. Syst. Evol. Res., 38 (4), 249–253.10.1046/j.1439-0469.2000.384150.x
Search in Google Scholar
Demeke, T., Ratnayaka, I., Phan, A. (2009). Effects of DNA extraction and purification methods on real-time quantitative PCR analysis of roundup ready soybean. J. Assoc. Offic. Anal. Chem. Int., 92 (4), 1136–1144.10.1093/jaoac/92.4.1136
Search in Google Scholar
Demeke, T., Ratnayaka, I., Holigroski, M., Phan, A. (2012). Assessment of DNA extraction methods for PCR testing of discontinued or unapproved biotech events in single seeds of canola, flax and soybean. Food Control, 24 (1–2), 44–49.10.1016/j.foodcont.2011.09.001
Search in Google Scholar
Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol.,3 (5), 294–299.
Search in Google Scholar
Galtier, N., Nabholz, B., Glémin, S., Hurst, G. D. (2009). Mitochondrial DNA as a marker of molecular diversity: A reappraisal. Mol. Ecol.,18 (22), 4541–4550.10.1111/j.1365-294X.2009.04380.x
Search in Google Scholar
Gavarāne, I., Kokina, I., Aksjuta, K., Barševskis, A., Valainis, U. (2011). Optimization of DNA extraction protocol for DNA isolation from air-dried collection material for further phylogenetic analysis (Coleoptera: Carabidae). Acta Biol. Univ. Daugavpils, 11 (2), 141–147.
Search in Google Scholar
Gilbert, M. T. P., Moore, W., Melchior, L., Worobey, M. (2007). DNA extraction from dry museum beetles without conferring external morphological damage. PLoS ONE (Public Library of Science One), 2 (3), e272.10.1371/journal.pone.0000272
Search in Google Scholar
Goldstein, P. Z., DeSalle R. (2003). Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Mol. Ecol.,12, 1993–1998.10.1046/j.1365-294X.2003.01860.x12803647
Search in Google Scholar
Harper, G. L., Maclean, N., Goulson, D. (2006). Analysis of museum specimens suggests extreme genetic drift in the Adonis blue butterfly (Polyommatus bellargus). Biol. J. Linn. Soc., 88, 447–452.10.1111/j.1095-8312.2006.00632.x
Search in Google Scholar
Hendrich, L., Pons, J., Ribera, I., Balke, M. (2010). Mitochondrial Cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates. PLoS ONE,5 (12), e14448.10.1371/journal.pone.0014448301097721203427
Search in Google Scholar
Howland, D. E., Hewitt, G. M. (1995). Phylogeny of the Coleoptera based on mitochondrial cytochrome oxidase I sequence data. Insect Mol. Biol., 4 (3), 203–215.10.1111/j.1365-2583.1995.tb00026.x8589847
Search in Google Scholar
Isaac, N. J. B., Mallet, J., Mace, G. M. (2004). Taxonomic inflation: Its influence on macroecology and conservation. Trends Ecol. Evol.,19 (9), 464–469.10.1016/j.tree.2004.06.00416701308
Search in Google Scholar
Kelly, R. P., Sarkar, I. N., Eernisse, J. D., Alle, D. R. (2007). DNA barcoding using chitons (genus Mopalia). Mol. Ecol. Notes,7, 177–183.10.1111/j.1471-8286.2006.01641.x
Search in Google Scholar
Kotze, J. D., Brandmayr, P., Casale, A., Dauffy-Richard, E., Dekoninck, W., Koivula, M. J., Lövei, G. L., Mossakowski, D., Noordijk, J., Paarmann, V., Pizzolotto, R., Saska, P., Schwerk, A., Serrano, J., Szyszko, J., Taboada, A., Turin, H., Venn, S., Vermeulen, R., Zetto, T. (2011) Forty years of carabid beetle research in Europe — from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation. ZooKeys,100, 55–148.10.3897/zookeys.100.1523313101221738408
Search in Google Scholar
Krishtalka, L., Peterson, T. D., Viegalis, J. B., Wiley, E. (2000). The green internet: A tool for conservation science. In: Conservation in the Internet Age: Strategic Threats and Opportunities (pp. 143–164). (J. Levitt, ed.). Island Press, Washington, DC.
Search in Google Scholar
Kubista, M., Andrade, J. M., Bengtsson, M., Forootan, A., Jonák, J., Lind, K., Sindelka, R., Sjöback, R., Sjögreen, B., Strömbom, L., Ståhlberg, A., Zoric, N. (2006). The real-time polymerase chain reaction. Mol. Aspects Med.,27 (2–3), 95–125.10.1016/j.mam.2005.12.00716460794
Search in Google Scholar
Lemey, P., Salemi, M., Vandamme, A. M. (2009). The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. New York: Cambridge University Press. 723 pp.10.1017/CBO9780511819049
Search in Google Scholar
Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature, 362, 709–715.10.1038/362709a08469282
Search in Google Scholar
Lueders, T., Friedrich, M. W. (2003). Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol.,69 (1), 320–326.10.1128/AEM.69.1.320-326.200315243112514011
Search in Google Scholar
Maddison, D. R., Baker, M. D., Ober, K. A. (1999). Phylogeny af carabid beetles as inferred 18S ribosomalDNA(Coleoptera: Carabidae). Systemat. Entomol.,24, 103–138.10.1046/j.1365-3113.1999.00088.x
Search in Google Scholar
Maddison, D. R., Moore, W., Baker, M. D., Ellis, T. M., Ober, K. A., Cannone, J. J., Gutell, R. R. (2009). Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae). Zool. Scr., 38 (1), 43–62.10.1111/j.1463-6409.2008.00359.x275290319789725
Search in Google Scholar
Mandrioli, M. (2008). Insect collections and DNA analyses: How to manage collections? Museum Management and Curatorship, 23, 193–199.10.1080/09647770802012375
Search in Google Scholar
Margam, V. M., Gachomo, E. W., Shukle, J. H., Ariyo, O. O., Seufferheld, M. J., Kotchoni, S. O. (2010). A simplified arthropod genomic-DNA extraction protocol for polymerase chain reaction (PCR)-based specimen identification through barcoding. Mol. Biol. Rep., 37, 3631–3635.10.1007/s11033-010-0014-520204529
Search in Google Scholar
Merzendorfer, H. (2013). Chitin synthesis inhibitors: Old molecules and new developments. Insect Sci.,20, 121–13810.1111/j.1744-7917.2012.01535.x23955853
Search in Google Scholar
Morlais, I., Severson, D. W. (2002). Complete mitochondrial DNA sequence and amino acid analysis of the cytochrome c oxidase subunit I (COI) from Aedes aegypti. DNA Res,,13, 123–127.10.1080/1042517029003005112180346
Search in Google Scholar
Muller, C. J., Beheregaray, L. B. (2010). Paleo island-affinities revisited biogeography and systematics of the Indo-Pacific genus Cethosia Fabricus (Lepidoptera: Nymphalidae). Mol. Phylogen. Evol., 57, 314–326.10.1016/j.ympev.2010.07.00220637292
Search in Google Scholar
Raupach, M. J., Astrin, J. J., Hanning, K., Peters K. M., Stoeckle, M. Y., Wägele, J. W. (2010). Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes. Front Zool.,7, 26.10.1186/1742-9994-7-26294534020836845
Search in Google Scholar
Rohland, N., Siedel, H., Hofreiter, M. (2004). Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. Biotechniques, 36 (5), 814–821.10.2144/04365ST0515152601
Search in Google Scholar
Sipos, R., Szekely, A. J., Palatinszky, M., Revesz, S., Marialigeti, K., Nikolausz, M. (2007). Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol., 60, 341–350.10.1111/j.1574-6941.2007.00283.x
Search in Google Scholar
Suarez, A. V., Tsutsui, N. D. (2004). The value of museum collections for research and society. BioOne, 54 (1), 66–74.10.1641/0006-3568(2004)054[0066:TVOMCF]2.0.CO;2
Search in Google Scholar
Sun, Y., Li, Q., Kong, L., Zheng, X. (2012). DNA barcoding of Caenogastropoda along coast of China based on the COI gene. Mol. Ecol. Res., 12, 209–218.10.1111/j.1755-0998.2011.03085.x
Search in Google Scholar
Thomsen, P. F., Elias, S., Gilbert, M. T. P., Haile, J., Munch, K., Kuzmina, S., Froese, G. D., Sher, A., Holdaway, N. R., Willerslev, E. (2009). Non-destructive sampling of ancient insect DNA. PLoS ONE,4 (4), e5048.10.1371/journal.pone.0005048
Search in Google Scholar
VanGuilder, H. D., Vrana, K. E., Freeman, W. M. (2008). Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques,44 (5), 619–626.10.2144/000112776
Search in Google Scholar
VanHardenbroek, M., Grocke, D. R., Sauer, P. E., Elias, S. A. (2012). North American transect of stable hydrogen and oxygen isotopes in water beetles from a museum collection. J. Paleolimnol., 48 (2), 461–470.10.1007/s10933-012-9623-4
Search in Google Scholar
Wandeler, P., Hoeck, P. E. A., Keller, L. F. (2007). Back to the future: Museum specimens in population genetics. Trends Ecol. Evol.. 22 (12), 634–642.10.1016/j.tree.2007.08.017
Search in Google Scholar
Watts, P. C., Thompson, J. D., Allen, K. A., Kemp, J. S. (2007). How useful is DNA extracted from the legs of archived insects for microsatellite-based population genetic analyses? J. Insect Conserv., 1, 195–198.10.1007/s10841-006-9024-y
Search in Google Scholar
Wiley, E. O., Lieberman, B. S. (2011). Phylogenetics: The Theory of Phylogenetic Systematics. New Jersey: John Wiley & Sons Inc. 406 pp.10.1002/9781118017883
Search in Google Scholar
Willerslev, E., Cooper, A. (2005). Ancient DNA. Proceedings of the Royal Society of London B,272, 3–16.
Search in Google Scholar
Willerslev, E., Hansen, A. J., Poinar, H. N. (2004). Isolation of nucleic acids and cultures from ice and permafrost. Trends Ecol Evol.,19, 141–147.10.1016/j.tree.2003.11.010
Search in Google Scholar
Winker, K. (2004). Natural history museums in a postbiodiversity era. Bio-Science, 54 (5), 455–459.10.1641/0006-3568(2004)054[0455:NHMIAP]2.0.CO;2
Search in Google Scholar
Wong, M. L., Medrano, J. F. (2005). Real-time PCR for mRNA quantitation. Biotechniques,39 (1), 75–85.10.2144/05391RV01
Search in Google Scholar
Yuan, J. S, Donglin, W., Stewart, C. N. (2008). Statistical methods for efficiency adjusted real-time PCR quantification. Biotechnol. J., 3 (1), 112–123.10.1002/biot.200700169
Search in Google Scholar
Yuan, J. S, Reed, A., Chen, F., Stewart C. N. (2006). Statistical analysis of real-time PCR data. BioMed Centr. Bioinformat.,7, 85.10.1186/1471-2105-7-85
Search in Google Scholar

Real-Time Polymerase Chain Reaction For Detection Of Optimal Thermal Profile For DNA Templates From Air-Dried Insect Collection Material

Abstract

Paradigm

My account