Forensic drowning site inference employing mixed pyrosequencing profile of DNA barcode gene (rbcL)

Abstract

The development of DNA barcoding method has given rise to a promising way of studying genetic taxonomy. Our previous study showed that pyrosequencing profile of 18S rDNA V7 hypervariable region can be used for identifying water sources without resolving the exact components of diatom colonies in water samples. In this continued study, we aimed to improve the established analysis method and to provide scientific evidence for forensic practices. A drowning animal model was set up by injecting mimic drowning fluid into the respiratory tract of the rabbit. In order to minimize the interference of animal DNA, the hypervariable region of chloroplast ribulose-1,5-bisphosphate carboxylase large unit gene (rbcL) was used as the pyrosequencing target region for the consistency analysis of plankton populations in tissues and water samples. After decoding the pyrosequencing profile of the targeted rbcL gene with the AdvISER-M-PYRO algorithm, the plankton colony that was inhaled into drowning animal lung tissue could be successfully traced back to the source of drowning fluid. Our data suggest that this method could be a reliable tool assisting forensic drowning site inference.

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References

  1. 1.

    Zhao Y, Chen X, Yang Y, Zhao X, Zhang S, Gao Z, Fang T, Wang Y, Zhang J (2018) Potential forensic biogeographic application of diatom colony consistency analysis employing pyrosequencing profiles of the 18S rDNA V7 region. Int J Legal Med 132(6):1611–1620. https://doi.org/10.1007/s00414-018-1849-x

    Article  Google Scholar 

  2. 2.

    Kakizaki E, Sonoda A, Sakai M, Yukawa N (2018) Simple detection of bacterioplankton using a loop-mediated isothermal amplification (LAMP) assay: first practical approach to 72 cases of suspected drowning. Forensic Sci Int 289:289–303. https://doi.org/10.1016/j.forsciint.2018.05.035

    CAS  Article  Google Scholar 

  3. 3.

    Kakizaki E, Ogura Y, Kozawa S, Nishida S, Uchiyama T, Hayashi T, Yukawa N (2012) Detection of diverse aquatic microbes in blood and organs of drowning victims: first metagenomic approach using high-throughput 454-pyrosequencing. Forensic Sci Int 220(1–3):135–146. https://doi.org/10.1016/j.forsciint.2012.02.010

    CAS  Article  Google Scholar 

  4. 4.

    He F, Huang D, Liu L, Shu X, Yin H, Li X (2008) A novel PCR-DGGE-based method for identifying plankton 16S rDNA for the diagnosis of drowning. Forensic Sci Int 176(2–3):152–156. https://doi.org/10.1016/j.forsciint.2007.08.005

    CAS  Article  Google Scholar 

  5. 5.

    Ambroise J, Deccache Y, Irenge L, Savov E, Robert A, Gala JL (2014) Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping. Bioinformatics 30(24):3590–3597. https://doi.org/10.1093/bioinformatics/btu516

    CAS  Article  Google Scholar 

  6. 6.

    Gamache J, Sun G (2015) Phylogenetic analysis of the genus Pseudoroegneria and the Triticeae tribe using the rbcL gene. Biochem Syst Ecol 62:73–81. https://doi.org/10.1016/j.bse.2015.07.038

    CAS  Article  Google Scholar 

  7. 7.

    Kawachi M, Ishimoto M, Mori F, Yumoto K, Sato M, Noël M-H (2013) MCC-NIES list of strains, 9th Edition. Tsukuba, Japan

  8. 8.

    Williams LG (1964) Possible relationships between plankton-diatom species numbers and water-quality estimates. Ecology 45(4):809–823. https://doi.org/10.2307/1934927

    Article  Google Scholar 

  9. 9.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. https://doi.org/10.1093/molbev/mst197

    CAS  Article  Google Scholar 

  10. 10.

    Reynolds CS (2006) Ecology of phytoplankton. Cambridge University Press, Cambridge

    Google Scholar 

  11. 11.

    Terazawa K, Takatori T (1980) Isolation of intact plankton from drowning lung tissue by centrifugation in a colloidal silica gradient. Forensic Sci Int 16(1):63–66. https://doi.org/10.1016/0379-0738(80)90180-2

    CAS  Article  Google Scholar 

  12. 12.

    Carballeira R, Vieira DN, Febrero-Bande M, Muñoz Barús JI (2018) A valid method to determine the site of drowning. Int J Legal Med 132(2):487–497. https://doi.org/10.1007/s00414-017-1708-1

    Article  Google Scholar 

  13. 13.

    Ago K, Hayashi T, Ago M, Ogata M (2011) The number of diatoms recovered from the lungs and other organs in drowning deaths in bathwater. Leg Med (Tokyo) 13(4):186–190. https://doi.org/10.1016/j.legalmed.2011.04.002

    Article  Google Scholar 

  14. 14.

    Yen LY, Jayaprakash PT (2007) Prevalence of diatom frustules in non-vegetarian foodstuffs and its implications in interpreting identification of diatom frustules in drowning cases. Forensic Sci Int 170(1):1–7. https://doi.org/10.1016/j.forsciint.2006.08.020

    Article  Google Scholar 

  15. 15.

    Yu Z, Liu C, Wang H, Chen L, Hu S, Zhao J (2014) The effect of enzyme digestion time on the detection of diatom species. Pak J Pharm Sci 27(3 Suppl):691–694

    PubMed  Google Scholar 

Download references

Acknowledgements

We thank Dr. John J Xin (Tufts University School of Medicine) for assistance in manuscript revision, as well as Miss Yue Zhang and Mr. Derek Xu (Brown University) for language editing.

Funding

This study was supported by grants from the National Natural Science Foundation of China (81630054, 81571861).

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Correspondence to Yufang Wang or Ji Zhang.

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Fang, T., Liao, S., Chen, X. et al. Forensic drowning site inference employing mixed pyrosequencing profile of DNA barcode gene (rbcL). Int J Legal Med 133, 1351–1360 (2019). https://doi.org/10.1007/s00414-019-02075-4

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Keywords

  • Forensic science
  • Drowning site inference
  • Diatom
  • Plankton
  • DNA barcode
  • rbcL
  • Pyrosequencing