Mycobacterium leprae DNS noteikšana arheoloģiskajās skeletālajās atliekās, izmantojot nākamās paaudzes sekvencēšanu
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Date
2021
Authors
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Volume Title
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Rīgas Stradiņa universitāte
Rīga Stradiņš University
Rīga Stradiņš University
Abstract
Līdz šim Baltijā nav bijuši ziņojumi par apstiprinātiem gadījumiem, ka arheoloģiskajā materiālā kādam indivīdam būtu konstatēta lepra. Tam par iemeslu varētu būt sarežģīta paleopatoloģiju noteikšana, ārējo pazīmju un kaulu materiāla bojājumu neviennozīmīgums, arheoloģisko izrakumu laikā nepilnīgi savāktie indivīdu kaulu komplekti, kā arī to sliktie saglabāšanās apstākļi Baltijas klimatisko apstākļu dēļ.
Šajā pētījumā, izmantojot nākamās paaudzes sekvencēšanu (NGS) un iegūto datu analizēšanu ar brīvpieejas interneta platformu biomedicīnisko datu analizēšanai usegalaxy.org. un programmatūru MALT, tika veikta senās DNS analīze un datu apstrāde, lai noskaidrotu Mycobacterium leprae DNS klātbūtni indivīda skeletālo atlieku fragmentos. Bioinformātiskas analīzes rezultāti neuzrādīja pārliecinošo senās M. leprae DNS klātbūtni arheoloģiskajā materiālā, kaut arī par lepras iespējamību liecināja indivīda vizuālā apskate arheoloģisko izrakumu veikšanas laikā. Veicot turpmāku datu analizēšanu, paraugā tika konstatēts Yersinia pestis DNS, kas liecina, ka atrastais indivīds savas dzīves laikā ir bijis slims ar mēri.
Until now, there have been no reports of a proven case of leprosy in the archaeological population in Baltic countires. This could be due to the complicated paleopathological analysis, indistinct sceletal damage, incomplete collection of individuals' set of bones during archaeological excavations, as well as poor conservation of ancient DNA due to the climate conditions of the Baltics. In this study, ancient DNA data processing was performed using next generation sequencing (NGS) and data analysis on a free-access Internet platform for analyzing biomedical data usegalaxy.org. and software MALT, to confirm the presence of Mycobacterium leprae DNA in fragments of the individual's skeletal remains. The results of the bioinformatical analysis did not indicated a clear link to ancient M. leprae DNA, although a case of leprosy was suggested after a visual inspection of the individual during archaeological excavations. When further analyzing the data, Yersinia pestis DNA was found in the sample, suggesting that this individual had been ill with the plague during his life.
Until now, there have been no reports of a proven case of leprosy in the archaeological population in Baltic countires. This could be due to the complicated paleopathological analysis, indistinct sceletal damage, incomplete collection of individuals' set of bones during archaeological excavations, as well as poor conservation of ancient DNA due to the climate conditions of the Baltics. In this study, ancient DNA data processing was performed using next generation sequencing (NGS) and data analysis on a free-access Internet platform for analyzing biomedical data usegalaxy.org. and software MALT, to confirm the presence of Mycobacterium leprae DNA in fragments of the individual's skeletal remains. The results of the bioinformatical analysis did not indicated a clear link to ancient M. leprae DNA, although a case of leprosy was suggested after a visual inspection of the individual during archaeological excavations. When further analyzing the data, Yersinia pestis DNA was found in the sample, suggesting that this individual had been ill with the plague during his life.
Description
Farmācija
Pharmacy
Veselības aprūpe
Health Care
Pharmacy
Veselības aprūpe
Health Care
Keywords
lepra; senā DNS; nākamās paaudzes sekvencēšana, leprosy; ancient DNA; next – generation sequencing