EDTA decalcification of dental calculus as an alternate means of microparticle extraction from archaeological samples

Tromp, Monica; Buckley, Hallie R.; Geber, Jonny; Matisoo‐Smith, Elizabeth

doi:10.1016/j.jasrep.2017.06.035

Cited by 25 publications

(32 citation statements)

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“…In this study, we evaluate whether using a modified version of the Method D protocol (henceforth Method H), with an initial EDTA wash and an extended digestion and decalcification step, results in improved endogenous aDNA recovery. In addition, because the majority of development in aDNA extraction protocols has been conducted with samples from temperate or cold contexts (Barlow et al, 2016;Boessenkool et al, 2016;Dabney et al, 2013a;Gamba et al, 2016;Gamba et al, 2014;) but see (Damgaard et al, 2015;Pinhasi et al, 2015;Tromp et al, 2017), this work focuses on protocol optimization with tooth and petrous portion samples recovered from tropical sites. Here we examine raw DNA yields and endogenous reads, recovered after shotgun Illumina sequencing from parallel, paired extractions and characterize differences in base pair composition, sequence read complexity, post-mortem damage profiles, and average read lengths recovered between the two methods.…”

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confidence: 99%

Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

Nieves-Colón

Ozga

Pestle

et al. 2017

Preprint

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Objectives:The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semitropical sites in Tanzania, Mexico, and Puerto Rico (N=12). Materials and Methods:All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.Results: No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.Discussion: Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/184119 doi: bioRxiv preprint first posted online 2 Ancient DNA (aDNA) is a low quality and low quantity source of genetic material, which is highly susceptible to external contamination (Gilbert et al., 2006;Hofreiter et al., 2001;Pääbo, 1989). Due to the variety of taphonomic and diagenetic processes that take place after death, DNA decays exponentially once cell repair functions cease in biological tissues (Hofreiter et al., 2001). Consequently, most genetic information obtained from ancient samples is contained in small, degraded DNA fragments (Allentoft et al., 2012;Briggs et al., 2007;Dabney et al., 2013a). Because of this, until recently, aDNA studies have focused on short but informative fragments of the autosomal genome or, alternatively, on multicopy loci such as mitochondrial DNA (Ho & Gilbert, 2010). Recent advances in DNA extraction, target enrichment, and nextgeneration sequencing methods now allow the recovery of complete genomes from remains dating as far back in time as the early Holocene and Middle Pleistocene (Meyer et al., 2016;Meyer et al., 2014;Orlando et al., 2013).Despite these improvements in stretching the time depth for aDNA recovery...

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confidence: 99%

Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

Nieves-Colón

Ozga

Pestle

et al. 2017

Preprint

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“…Microparticles were extracted from 42 dental calculus samples (on average ∼3 × 3 mm) using the ethylenediaminetetraacetic acid (EDTA) extraction method described in Tromp et al (43) and briefly reviewed in SI Appendix. Starch granules were analyzed primarily using published studies and descriptions (24,(44)(45)(46)(47)(48)(49)(50) as well as a reference collection; measurements and descriptions of relevant taxa are included in Dataset S3.…”

Section: Methodsmentioning

confidence: 99%

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine

Geber

Tromp

Ashley

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually the only means of subsistence—the potato crop—for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid–19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39′ N, −7°15′ W). The results corroborate the historical accounts of food provisions before and during the famine, with evidence of corn (maize), potato, and cereal starch granules from the microparticle analysis and milk protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein—a food source generally reserved only for export and the better-off social classes—which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability.

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“…A partir da placa supragengival e com o favorecimento do pH alcalino, o cálculo dentário (Figura 3) forma-se através de sais minerais provenientes da saliva, que precipitam e formam um material duro, mineralizado e rugoso, atuando como facilitador para o acúmulo de mais placa. Esta estrutura potencializa os efeitos patogênicos da placa bacteriana (CARRANZA et al, 2012;KOUKI et al, 2013;TROMP et al, 2017).…”

Section: Etiologia E Fisiopatologiaunclassified

“…Com a progressão do contínuo estímulo inflamatório a partir da placa instalada, ocorrem alterações degenerativas no epitélio juncional que levam à migração deste, dando origem a diversas características clínicas (CARRANZA et al, 25 2012;TROMP et al, 2017). Devido a importância da integridade do epitélio juncional para a preservação da doença periodontal, faz-se necessário compreender alguns critérios de caracterização clínica referentes à sua migração, como retração gengival (Figura 4), bolsa periodontal (Figuras 5 e 6) e exposição de furca (Figura 7) (GORREL, 2010).…”

Section: Etiologia E Fisiopatologiaunclassified

“…Além desta média, a profundidade resultante da sondagem periodontal determina migração do epitélio juncional, destruição do ligamento periodontal e reabsorção do osso alveolar (GORREL, 2010). Logo, a bolsa periodontal define-se clinicamente como um sulco gengival patologicamente aprofundado, sendo uma característica importante desta doença (CARRANZA et al, 2012;TROMP et al, 2017).…”

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<b>Desenvolvimento e validação de uma cartilha educativa sobre a doença periodontal em cães e gatos</b>

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EDTA decalcification of dental calculus as an alternate means of microparticle extraction from archaeological samples

Cited by 25 publications

References 29 publications

Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine

<b>Desenvolvimento e validação de uma cartilha educativa sobre a doença periodontal em cães e gatos</b>

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