Sequencing human mitochondrial hypervariable region II as a molecular fingerprint for environmental waters

Environmental Science and Technology

Volumn 48, Issue 18, 2014, Pages 10648-10655

  Kapoor, Vikram ^a   DeBry, Ronald W ^b   Boccelli, Dominic L ^a   Wendell, David ^a  

^a University of Cincinnati   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MAMMALS; MITOCHONDRIA;

BACTERIAL INDICATORS; COMBINED SEWER OVERFLOWS; ENVIRONMENTAL WATER; FECAL CONTAMINATION; HIGH-THROUGHPUT SEQUENCING; IDENTIFICATION METHOD; MOLECULAR FINGERPRINT; POPULATION DIVERSITY;

CONTAMINATION;

MITOCHONDRIAL DNA; WATER; FRESH WATER; SEWAGE;

BACTERIUM; BIOINDICATOR; BIOMARKER; FECES; IDENTIFICATION METHOD; MAMMAL; MITOCHONDRIAL DNA; POLLUTANT SOURCE; SEWAGE; SPATIAL RESOLUTION; TRACKING; URBAN REGION; WATER POLLUTION; WATERSHED;

AMPLICON; ARTICLE; BIOINFORMATICS; CATCHMENT; DNA CONTAMINATION; FINGER DERMATOGLYPHICS; GENE FREQUENCY; HIGH THROUGHPUT SEQUENCING; HUMAN; INDEL MUTATION; METAGENOMICS; MITOCHONDRIAL HAPLOGROUP; MITOCHONDRIAL HYPERVARIABLE REGION II; MITOCHONDRION; SINGLE NUCLEOTIDE POLYMORPHISM; WATERSHED; ANALYSIS; ANIMAL; ENVIRONMENTAL MONITORING; FECES; GENETICS; MICROBIOLOGY; PROCEDURES; SEWAGE; UNITED STATES; URBANIZATION; WATER POLLUTION;

BACTERIA (MICROORGANISMS); MAMMALIA;

ANIMALS; DNA, MITOCHONDRIAL; ENVIRONMENTAL MONITORING; FECES; FRESH WATER; HUMANS; OHIO; POLYMORPHISM, SINGLE NUCLEOTIDE; SEWAGE; URBANIZATION; WATER MICROBIOLOGY; WATER POLLUTION;

EID: 84924794718     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es503189g     Document Type: Article

References (51)

1. Caldwell, J. M.; Raley, M. E.; Levine, J. F. Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents. Environ. Sci. Technol. 2007, 41(9), 3277-3283.
2. Kapoor, V.; Smith, C.; Santo Domingo, J. W.; Lu, T.; Wendell, D. Correlative assessment of fecal indicators using human mitochondrial DNA as a direct marker. Environ. Sci. Technol. 2013, 47(18), 10485-10493.
3. Vuong, N.-M.; et al. Fecal source tracking in water using a mitochondrial DNA microarray. Water Res. 2012, 47(1), 16-30.
4. Gordon, D. M. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiology 2001, 147(5), 1079-1085.
5. Anderson, K. L.; Whitlock, J. E.; Harwood, V. J. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl. Environ. Microbiol. 2005, 71(6), 3041-3048.
6. Glassmeyer, S. T.; et al. Transport of chemical and microbial compounds from known wastewater discharges: Potential for use as indicators of human fecal contamination. Environ. Sci. Technol. 2005, 39(14), 5157-5169.
7. Hagedorn, C.; Weisberg, S. B. Chemical-based fecal source tracking methods: Current status and guidelines for evaluation. Rev. Environ. Sci. Biotechnol. 2009, 8(3), 275-287.
8. Martellini, A.; Payment, P.; Villemur, R. Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Res. 2005, 39(4), 541-548.
9. Budowle, B.; Allard, M. W.; Wilson, M. R.; Chakraborty, R. Forensics and mitochondrial DNA: Applications, debates, and foundations. Annu. Rev. Genomics Hum. Genet. 2003, 4(1), 119-141.
10. Wilson, M. R.; DiZinno, J. A.; Polanskey, D.; Replogle, J.; Budowle, B. Validation of mitochondrial DNA sequencing for forensic casework analysis. Int. J. Legal Med. 1995, 108(2), 68-74.
11. Gill, P.; et al. Identification of the remains of the Romanov family by DNA analysis. Nat. Genet. 1994, 6(2), 130-135.
12. Ingman, M.; Kaessmann, H.; PaÈaÈbo, S.; Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 2000, 408(6813), 708-713.
13. Wallace, D. C. Mitochondrial DNA sequence variation in human evolution and disease. Proc. Natl. Acad. Sci. U. S. A. 1994, 91(19), 8739-8746.
14. Salas, A.; Lareu, V.; Calafell, F.; Bertranpetit, J.; Carracedo, A. mtDNA hypervariable region II (HVII) sequences in human evolution studies. Eur. J. Human Genet. 2000, 8(12), 964-974.
15. Krings, M.; Geisert, H.; Schmitz, R. W.; Krainitzki, H.; Pääbo, S. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl. Acad. Sci. U. S. A. 1999, 96(10), 5581-5585.
16. Ovchinnikov, I. V.; et al. Molecular analysis of neanderthal DNA from the northern Caucasus. Nature 2000, 404(6777), 490-493.
17. Schlebusch, C. M.; Lombard, M.; Soodyall, H. MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa. BMC Evol. Biol. 2013, 13(1), 56.
18. Byrne, E. M.; et al. The use of common mitochondrial variants to detect and characterise population structure in the Australian population: implications for genome-wide association studies. Eur. J. Human Genet. 2008, 16(11), 1396-1403.
19. Burgess, D. J. Disease genetics: Double danger from mitochondrial mutations. Nature Rev. Genet. 2013, 14(10), 678-679.
20. Wallace, D. C. Mitochondria and cancer. Nature Rev. Cancer 2012, 12(10), 685-698.
21. Langille, M. G.; et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 2013, 31(9), 814-821.
22. Yergeau, E.; et al. Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl. Environ. Microbiol. 2012, 78(21), 7626-7637.
23. Marsalek, J.; Rochfort, Q. Urban wet-weather flows: Sources of fecal contamination impacting on recreational waters and threatening drinking-water sources. J. Toxicol. Environ. Health, Part A 2004, 67(20-22), 1765-1777.
24. Kamra, A.; et al. Exfoliated colonic epithelial cells: Surrogate targets for evaluation of bioactive food components in cancer prevention. J. Nutr. 2005, 135(11), 2719-2722.
25. Albaugh, G. P.; et al. Isolation of exfoliated colonic epithelial cells, a novel, non-invasive approach to the study of cellular markers. Int. J. Cancer 1992, 52(3), 347-350.
26. Andreasson, H.; Gyllensten, U.; Allen, M. Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques 2002, 33(2), 402-411.
27. Higuchi, R.; von Beroldingen, C. H.; Sensabaugh, G. F.; Erlich, H. A. DNA typing from single hairs. Nature 1988, 332(6164), 543-546.
28. Soller, J. A.; Schoen, M. E.; Bartrand, T.; Ravenscroft, J. E.; Ashbolt, N. J. Estimated human health risks from exposure to recreational waters impacted by human and non-human sources of faecal contamination. Water Res. 2010, 44(16), 4674-4691.
29. Parsons, T. J.; et al. A high observed substitution rate in the human mitochondrial DNA control region. Nat. Genet. 1997, 15, 363-368.
30. Meyer, S.; Weiss, G.; von Haeseler, A. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 1999, 152(3), 1103-1110.
31. van Oven, M.; Kayser, M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 2009, 30(2), E386-E394.
32. U. S. Environmental Protection Agency. (2009) Biological and Water Quality Study of the Lower Little Miami River and Selected Tributaries. OHIO EPA Technical Report EAS/2009-10-06.
33. Hutter, G.; et al. Use of polymorphisms in the noncoding region of the human mitochondrial genome to identify potential contamination of human leukemia-lymphoma cell lines. Hematol. J. 2004, 5(1), 61-68.
34. Andrews, R. M.; et al. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 1999, 23(2), 147-147.
35. Brandon, M. C.; et al. MITOMAP: A human mitochondrial genome database.2004 update. Nucleic Acids Res. 2005 33(suppl1), D611-D613.
36. Ingman, M.; Gyllensten, U. mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res. 2006 34(suppl 1), D749-D751.
37. Parson, W.; Dür, A. EMPOP.A forensic mtDNA database. Forensic Sci. Int. Genet. 2007, 1(2), 88-92.
38. Brandon, M. C.; et al. MITOMASTER: A bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum. Mutat. 2009, 30(1), 1-6.
39. Parson, W.; et al. Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci. Int. Genet. 2013, 7(5), 543-549.
40. Seo, S. B.; et al. Single nucleotide polymorphism typing with massively parallel sequencing for human identification. Int. J. Legal Med. 2013, 127(6), 1079-1086.
41. Whiteley, A. S.; et al. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J. Microbiol. Methods 2012, 91(1), 80-88.
42. Li, H.; Homer, N. A survey of sequence alignment algorithms for next-generation sequencing. Briefs Bioinform. 2010, 11(5), 473-483.
43. Altshuler, D.; et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 2000, 407(6803), 513-516.
44. Li, M.; et al. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am. J. Hum. Genet. 2010, 87(2), 237-249.
45. Stewart, J.; et al. Length variation in HV2 of the human mitochondrial DNA control region. J. Forensic Sci. 2001, 46(4), 862-870.
46. Lee, C.; Mándoiu, I. I.; Nelson, C. E. Inferring ethnicity from mitochondrial DNA sequence. BMC Proc. 2011, 5(2), S11.
47. Wallace, D. C.; Brown, M. D.; Lott, M. T. Mitochondrial DNA variation in human evolution and disease. Gene 1999, 238(1), 211-230.
48. Cincinnati Census Data Website; http://www.cincinnati-oh.gov/planning/reports-data/census-demographics.
49. Taylor, R. W.; Turnbull, D. M. Mitochondrial DNA mutations in human disease. Nat. Rev. Genet. 2005, 6(5), 389-402.
50. Wallace, D. C. Mitochondrial genetics: A paradigm for aging and degenerative diseases? Science 1992, 256(5057), 628-632.
51. Shen, E. Z.; et al. Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans. Nature 2014, 508(7494), 128-132.