Fisheries and Aquatic Sciences

The Korean Society of Fisheries and Aquatic Science (한국수산과학회)
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Development of Clamping Probe for Rare DNA Detection using Universal Primers

  • Kim, Meyong Il (Incheon Fisheries Research Institute) ;
  • Lee, Ki-Young (Department of Marine Biotechnology, Kunsan National University) ;
  • Cho, Sang-Man (Department of Aquaculture and Aquatic resources, Kunsan National University)
  • Received : 2014.03.05
  • Accepted : 2014.05.21
  • Published : 2014.09.30
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Abstract

PCR amplification with universal primer is a useful tool for speciation of symbionts in marine eukaryote coupled with robust separation method such as denaturing high performance chromatography (DHPLC). To overcome the biased amplification, clamping PCR is recommended to suppress the amplification of host gene. In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis: C3 linked nucleotide (C3) and peptide nucleic acid (PNA). PNA was 3-4 orders of magnitude higher than that of C3 tested in clamping efficiency and rare gene detection. This represented that PNA could be a more competent clamping probe for the enhancement of PCR amplification for rare symbiont genes.

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References

  1. Amann R and Ludwig W. 2000. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24, 555-565. https://doi.org/10.1111/j.1574-6976.2000.tb00557.x
  2. Baker GC, Smith JJ and Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. J Microbiol Meth 55, 541-555. https://doi.org/10.1016/j.mimet.2003.08.009
  3. Bass D and Cavalier-Smith T. 2004. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int J Syst Evol Microbiol 54, 2393-2404. https://doi.org/10.1099/ijs.0.63229-0
  4. Blankenship LE and Yayanos AA. 2005. Universal primers and PCR of gut contents to study marine invertebrate diets. Mol Ecol 14, 891-899. https://doi.org/10.1111/j.1365-294X.2005.02448.x
  5. Bottger EC. 1989. Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol Lett 65, 171-176. https://doi.org/10.1111/j.1574-6968.1989.tb03617.x
  6. Cho SM. 2012. Development of Denaturing High-Performance Liquid Chromatography (DHPLC) Assay to detect parasite infection in Grass shrimp, Palaemonetes pugio. Fish Aquat Sci 15, 107-115.
  7. Cunningham CO. 2002. Molecular diagnosis of fish and shellfish diseases: present status and potential use in disease control. Aquaculture 206, 19-55. https://doi.org/10.1016/S0044-8486(01)00864-X
  8. Dames S, Margraf RL, Pattison DC, Wittwer CT and Voelkerding KV. 2007. Characterization of aberrant melting peaks in unlabeled probe assays. J Mol Diagn 9, 290-296. https://doi.org/10.2353/jmoldx.2007.060139
  9. Demers DB, Curry ET, Egholm M and Sozer AC. 1995. Enhanced PCR Amplification of VNTR Locus D1s80 Using Peptide Nucleic-Acid (PNA). Nucleic Acids Res 23, 3050-3055. https://doi.org/10.1093/nar/23.15.3050
  10. Demidov VV and Frank-Kamenetskii MD. 2004. Two sides of the coin: affinity and specificity of nucleic acid interactions. Trends Biochem Sci 29, 62-71. https://doi.org/10.1016/j.tibs.2003.12.007
  11. Frischer, ME, Danforth JM and Tyner LC. 2000. Development of an Argopecten-specific 18S rRNA targeted genetic probe. Mar Biotechnol 2, 11-20.
  12. Frishcer, M, Hansen A, Wylie J, Wimbush J, Murray J and Nierzwicki-Bauer S. 2002. Specific amplification of the 18S rRNA gene as a method to detect zebra museel (Dreissena polymorpha) larvae in plankton samples. Hydrobiol 487, 33-44. https://doi.org/10.1023/A:1022971918673
  13. Gruebl T, Frischer ME, Sheppard M, Neumann M, Maurer AN and Lee RF. 2002. Development of an 18S rRNA gene-targeted PCR-based diagnostic for the blue crab parasite Hematodinium sp. Dis Aquat Organ 49, 61-70. https://doi.org/10.3354/dao049061
  14. Iwen PC, Hinrichs SH and Rupp ME. 2002. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 40, 87-109. https://doi.org/10.1080/mmy.40.1.87.109
  15. Jury F, Bueid A, Ollier W, Fox A and Upton M. 2007. Analysis of mixed microbial species in clinically relevant biofilms using denaturing HPLC. In. ICC, Munich, Germany, pp. S394.
  16. Karkare S and Bhatnagar D. 2006. Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Appl Microbiol Biotechnol 71, 575-586. https://doi.org/10.1007/s00253-006-0434-2
  17. Kim Y, Powell EN, Wade TL and Presley BJ. 2008. Relationship of parasites and pathologies to contaminant body burden in sentinel bivalves: NOAA Status and Trends 'Mussel Watch' Program. Mar Environ Res 65, 101-127. https://doi.org/10.1016/j.marenvres.2007.09.003
  18. Kuris AM, Hechinger RF, Shaw JC, Whitney KL, Aguirre-Macedo L, Boch CA, Dobson AP, Dunham EJ, Fredensborg BL, Huspeni TC, Lorda J, Mababa L, Mancini FT, Mora AB, Pickering M, Talhouk NL, Torchin ME and Lafferty KD. 2008. Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nature 454, 515-518. https://doi.org/10.1038/nature06970
  19. Lafferty KD and Kuris AM. 1999. How environmental stress affects the impacts of parasites. Limnol Oceanogr 44, 925-931. https://doi.org/10.4319/lo.1999.44.3_part_2.0925
  20. Lightner DV and Redman RM. 1998. Shrimp diseases and current diagnostic methods. Aquaculture 164, 201. https://doi.org/10.1016/S0044-8486(98)00187-2
  21. Lin HW, Yin JH, Lo JP, Wang YH, Lee SY and Lu JJ. 2004. Use of universal polymerase chain reaction assay and endonuclease digestion for rapid detection of Neisseria meningitides. J Microbiol Immunol Infect 37, 371-374.
  22. Moller H. 1987. Pollution and parasitism in the aquatic environment. Int J Parasitol 17, 353-361. https://doi.org/10.1016/0020-7519(87)90110-X
  23. Mohlenhoff P, Muller L, Gorbushina AA and Petersen K. 2001. Molecular approach to the characterisation of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects. FEMS Microbiol Lett 195, 169-173. https://doi.org/10.1111/j.1574-6968.2001.tb10516.x
  24. Mothershed EA and Whitney AM. 2006. Nucleic acid-based methods for the detection of bacterial pathogens: present and future considerations for the clinical laboratory. Clin Chim Acta 363, 206-220. https://doi.org/10.1016/j.cccn.2005.05.050
  25. Nielsen PE and Egholm M. 1999. An Introduction to Peptide Nucleic Acid. Current Issues Molec Biol 1, 89-104.
  26. Orum H. 2000. PCR clamping. Curr Issues Mol Biol 2, 27-30.
  27. Pineau P, Henry M, Suspe'Ne R, Marchio A, Dettai A, Debruyne R, Petit T, Le'Cu A, Moisson P, Dejean A, Wain-Hobson S and Vartanian J-P. 2004. A Universal Primer Set for PCR Amplification of Nuclear Histone H4 Genes from All Animal Species. Mol Biol Evol 22, 582-588. https://doi.org/10.1093/molbev/msi053
  28. Schmidt TM and Relman DA. 1994. Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods Enzymol 235, 205-222. https://doi.org/10.1016/0076-6879(94)35142-2
  29. Shakeel S, Karim S and Ali A. 2006. Peptide nucleic acid (PNA) - a review. J Chem Technol Biot 81, 892-899. https://doi.org/10.1002/jctb.1505
  30. Sherwood AR and Presting GG. 2007. Universal primers amplify a 23s rDNA plastid marker in eukaryotic algae and cyanobacteria. J Phycol 43, 605-608. https://doi.org/10.1111/j.1529-8817.2007.00341.x
  31. Thakur NL, Jain R, Natalio F, Hamer B, Thakur AN and Muller WE. 2008. Marine molecular biology: an emerging field of biological sciences. Biotechnol Adv 26, 233-245. https://doi.org/10.1016/j.biotechadv.2008.01.001
  32. Tian YJ, Yang H, Wu XJ and Li DT. 2005. Molecular analysis of microbial community in a groundwater sample polluted by landfill leachate and seawater. J Zhejiang Univ Sci B 6, 165-170.
  33. Troedsson C, Lee RF, Stokes V, Walters TL, Simonelli P and Frischer ME. 2008a. Development of a denaturing high-performance liquid chromatography method for detection of protist parasites of metazoans. Appl Environ Microbiol 74, 4336-4345. https://doi.org/10.1128/AEM.02131-07
  34. Troedsson C, Lee RF, Walters T, Stokes V, Brinkley K, Naegele V and Frischer ME. 2008b. Detection and discovery of crustacean parasites in blue crabs (Callinectes sapidus) by using 18S rRNA gene-targeted denaturing high-performance liquid chromatography. Appl Environ Microbiol 74, 4346-4353. https://doi.org/10.1128/AEM.02132-07
  35. Vestheim H and Jarman SN. 2008. Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs. Front Zool 5, 12. https://doi.org/10.1186/1742-9994-5-12