Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach

Iñiguez, Alena Mayo; Araújo, Adauto; Ferreira, Luiz Fernando; Vicente, Ana Carolina Paulo

doi:10.1590/s0074-02762003000900012

Cited by 35 publications

(29 citation statements)

References 18 publications

(15 reference statements)

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“…This aDNA damage results in absent bands (=allelic dropouts) or in artificial bands, produced by the presence of co-extracted contaminating modern or archaeological plant material or by polyploidy or gene duplication. Nevertheless, some reports have been published (Siles et al 2000;Suh et al 2000;Iniguez et al 2003;Gyulai et al 2006).…”

Section: Methodsmentioning

confidence: 99%

“…aDNA analyses of complex plant mixtures, as found for example in faeces (Poinar et al 1998;Hofreiter et al 2000;Poinar et al 2001;Kuch et al 2002;Hofreiter et al 2003;Iniguez et al 2003), demonstrate the potential of aDNA studies and of collaboration between geneticists and morphologists for the reconstruction of diet. Even more information has been gained from faeces by employing both types of investigation.…”

Section: Vegetation and Dietmentioning

confidence: 98%

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Ancient plant DNA in archaeobotany

Schlumbaum

Tensen

Jaenicke-Després

2007

Veget Hist Archaeobot

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Plant diaspores, tissues and wood are preserved in natural and anthropogenic sediments. Also, over the past centuries, plants have been collected in herbaria. These plant remains carry macroscopic and molecular information, making them a rich source for reconstructing past plant use, agriculture, diet or vegetation-they are thus proxies for past economies, ecology, migrations or trade. This article focuses on the application of ancient DNA analyses from plants excavated at Holocene archaeological sites. A short methodological section is added to illustrate possibilities and limitations of ancient DNA research in plants.

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Section: Methodsmentioning

confidence: 99%

Section: Vegetation and Dietmentioning

confidence: 98%

Ancient plant DNA in archaeobotany

Schlumbaum

Tensen

Jaenicke-Després

2007

Veget Hist Archaeobot

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“…These approaches have been applied by us, and others, in paleogenetic studies [17,31,32, 56–58]. We chose to use the WGA based on MDA technology which uses a Phi29 polymerase which has 3'→5' exonuclease activity and a higher fidelity during replication compared to Taq DNA polymerase (qiagen.com).…”

Section: Resultsmentioning

confidence: 99%

“…We implemented standard aDNA procedures to avoid aDNA degradation, contamination from modern DNA, and cross-contamination during the paleogenetic analysis as described [31–33]. The preparation of samples, aDNA extraction, and PCR were performed in the Paleogenetic Laboratory (LABTRIP/IOC/FIOCRUZ) in an isolated environment, in facilities exclusively dedicated to aDNA research.…”

Section: Methodsmentioning

confidence: 99%

Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara

Guedes

Jaeger

Líryo³

et al. 2018

PLoS ONE

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Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.

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“…It harnesses DNA polymerase I derived from E. coli to synthesize new strands and T4 DNA ligase to seal the nicks [16], and may be accompanied by a pretreatment step with PNK and AP endonuclease I in order to guarantee the presence of the necessary termini [54]. Several studies have utilized the method [10,55] and some have stepped it up to tackle other lesions. Di Bernardo et al for one have taken advantage of the interstrand cross-links in aDNA and applied polymerization repair to retrieve the respective sequences.…”

Section: Improving Dna Amplification Yield: the Approachesmentioning

confidence: 99%

Raman Spectroscopy: A Promising Technique for Analyzing Nucleic Acid Refractory to PCR Amplification

Matar¹,

Merheb²

2014

TOSPECJ

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Ancient DNA (aDNA) refers to the genetic material found in dead paleontological and archeological samples. Being subject to various types of stressors, it undergoes different hydrolytic and oxidative post mortem modifications that result in the formation of DNA lesions. These lesions are found to either block the DNA polymerase during replication or induce nucleotide misincorporations. Besides, aDNA samples occur in minimal quantities; which represents an additional obstacle that researchers have to overcome in order to study aDNA. The earliest major efforts included the use of molecular cloning and polymerase chain reaction (PCR) to amplify aDNA sequences. These techniques were later found to be associated with a number of false results and unauthentic findings. There have been numerous attempts to eliminate the shortcomings of PCR and improve the quality of aDNA through avoiding contamination, repairing lesions, using translesion polymerases, etc. However, the majority of these have failed to yield accurate and specific results. Surfaceenhanced resonance Raman scattering (SERRS), on the other hand, starts in the right foot by introducing a sensitive nonenzymatic approach for the specific detection of single-and double-stranded DNA. The ability of this method to evade DNA degradation is particularly important for not only studying aDNA, but also analyzing DNA refractory to PCR amplification in processed products.

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Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach

Cited by 35 publications

References 18 publications

Ancient plant DNA in archaeobotany

Ancient plant DNA in archaeobotany

Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara

Raman Spectroscopy: A Promising Technique for Analyzing Nucleic Acid Refractory to PCR Amplification

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