Abstract Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.
Tuberculosis (TB) was a large burden of infections that peaked during the 19th century in Europe. Mummies from the 18th century CE, discovered in the crypt of a church at Vác, Hungary, had high TB prevalence, as revealed by amplification of key fragments of TB DNA and genome-wide TB analysis. Complementary methods are needed to confirm these diagnoses and one approach uses the identification of specific lipid biomarkers, such as TB mycocerosic acids (MCs). Previously, MC derivatives were profiled by specialised gas chromatography-mass spectrometry (GC-MS), so an alternative more direct approach has been developed. Underivatized MCs are extracted and analysed by high-performance liquid chromatography linked to a mass spectrometer, in heated electrospray ionisation mode (HPLC-HESI-MS). The method was validated using representatives of the Mycobacterium tuberculosis complex and other mycobacteria and tested on six Vác mummy cases, previously considered positive for TB infection. Analysing both rib and soft tissue samples, four out of six cases gave profiles of main C32 and major C29 and C39 mycocerosates correlating well with those of M. tuberculosis. Multidisciplinary methods are needed in the diagnosis of ancient tuberculosis; this new protocol accesses important confirmatory evidence, as demonstrated by the confirmation of TB in the Vác mummies.
Összefoglaló. Bevezetés: Egy traumás eredetű sérüléseket mutató, ókori egyiptomi koponya vizsgálatát ismertetjük a Magyar Természettudományi Múzeum gyűjteményéből. A jelen cikkben egy mumifikált fej elemzését emeltük ki, ennek átfogó vizsgálatát és részletes eredményeit közöljük. Célkitűzés: Célunk egy multidiszciplináris vizsgálatsorozat megvalósítása volt, amelyen keresztül képet kapunk az egykor Egyiptom területén élt emberek egészségi állapotáról. Módszer: A kutatás során a múmiákon szerves és szervetlen kémiai analíziseket, komputertomográfiai és röntgenvizsgálatot, szénizotópos kormeghatározást végeztünk, és felhasználtunk biológiai antropológiai módszereket is. Eredmények: A koponya igazoltan az ókori Egyiptomból származik, és mivel sebei gyógyulásnak indultak, véleményünk szerint az egyén túlélte a fejét ért behatást. Ez meglepő eredménynek minősül, hiszen ilyen jellegű életveszélyes traumás sérüléseket csak akkor lehet nagy valószínűséggel túlélni, ha megfelelő orvosi ellátás áll rendelkezésre. Következtetés: Úgy gondoljuk, ebben az esetben is ez történt, bizonyítva, hogy az egyiptomi orvosi ismeretek valóban igen fejlettek és az orvoslás magas színvonalú volt. Orv Hetil. 2020; 161(51): 2162–2170. Summary. Introduction: We are presenting the analysis of an ancient Egyptian mummified head from the collection of the Hungarian Natural History Museum, which shows special traumatic injuries. The examination of this artefact nicely demonstrates the procedures we usually apply in our research on the Egyptian mummies of the Museum. Objective: Our aim was to implement a series of multidisciplinary studies to get a picture of the health condition of these people once living in the territory of Egypt. Method: When researching the mummies, we performed organic and non-organic chemical analyses, computed tomography, X-ray examinations, radiocarbon isotope dating as well as biological anthropological methods. Results: In this article, we report on the comprehensive examination of the skull and the detailed results we got. The skull is proven to originate from ancient Egypt. Conclusion: As the wounds began to heal, we can conclude that the individual survived the impact on his head. This is quite surprising as such life-threatening traumatic injuries can only be survived if adequate medical care is available. We believe this was the case also here, i. e., ancient Egyptian medicine was highly developed and of really high standards. Orv Hetil. 2020; 161(51): 2162–2170.
A fertőző megbetegedesek paleopatologiai rekonstrukcioja az utobbi evtizedek kiemelt jelentősegű kutatasi iranyvonala volt mind a magyarorszagi, mind a nemzetkozi paleopatologiai kutatasban. A kutatasokat a vaci Feherek templomanak kriptajabol feltart termeszetesen mumifikalodott emberi maradvanyon vegeztuk. A kutatas anyaga egyedulallo lehetőseget biztositott abban a tekintetben, hogy egy viszonylag rovid időszak nepesseget reprezentalja, meglehetősen nagy egyedszammal (n=265). Fontos kiemelni, hogy a modern orvosi ellatas miatti szelekcio nem ervenyesult a vizsgalt nepessegcsoportnal. A kutatas soran egy ősi, a gyogyszerek es a modern orvosi műkodes hatasatol mentes populacio eseteben vegeztunk vizsgalatokat tobb, betegsegre hajlamosito polimorfizmus, ill. nehany kronikus betegsegben szenvedőkben halmozottan előfordulo patogen tekinteteben. Ugyancsak celunk volt a nepessegcsoport multidiszciplinaris, mikro-torteneti, biologiai-patologiai rekonstrukcioja, egeszsegugyi helyzetenek felterkepezese. | One of the key topics of the worlds’ leading palaeopathological researches has been the reconstruction of past epidemics. The multidisciplinary research was done on the naturally mummified bodies came to light in the Dominican Church of Vac, Hungary. With the study of a population lived before the era of extensive use of antibiotics and modern medicines, we aimed to learn about polymorphism related to disease susceptibilities and some pathogens frequently occur in ill patients. Our research is unique in focusing on a fairly large population (n=265) restricted to a rather short period, incorporating its degree of infection by the selected microorganisms, detection of enzyme polymorphisms related to disease susceptibilities, and population genetic studies. We aimed to make micro-historical, biological-pathological reconstruction of the 18th century population, to figure out their health conditions with multidisciplinary approach.
Abstract Reconstructing premortem DNA methylation levels in ancient DNA (aDNA) has led to breakthrough studies such as the prediction of anatomical features of the Denisovan, as well as the castration status of ancient horses. These studies relied on computationally inferring methylation levels from damage signals in naturally deaminated cytosines. Because of statistical constraints, this inference requires high-coverage sequencing, and is thus not only expensive but also restricted to samples with exceptional DNA preservation. Instead, a method to directly measure methylation levels in aDNA, as exists in modern DNA samples, would open the door to a more thorough and cost effective ability to study ancient DNA methylation. We have tested two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. We find that both methods preserve sufficient DNA yields to allow for methylation measurement. Bisulfite treatment, combined with a single stranded library preparation, shows the least reduction in DNA yields compared to no methylation treatment, as well as the least biases during methylation conversion. In addition, we show that applying bisulfite treatment to ∼0.4-fold coverage sample provides a methylation signal that is comparable to, or even better, than the computationally inferred one. We thus present a method to directly measure methylation in ancient DNA that is cost effective and can be used on a wide variety of ancient samples.
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