Abstract
The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and ...molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and – as a result of salt emanating from the walls – on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors.
Nucleic acid extraction from complex environmental and ancient tissue material is prone to co‐extract inhibitory substances that make further molecular analysis difficult or impossible. This ...co‐extraction occurs in both solid‐phase and liquid‐phase/organic nucleic acid extraction protocols. Currently, the widely used method to overcome inhibition includes the addition of bovine serum albumin (BSA) to the downstream enzymatic reactions or the dilution of the nucleic acid extracts. BSA, however, seems to reduce the inhibitory effect of certain compounds only, and excessive dilution may change the original DNA composition.
In this study, we introduce an innovative new method using linear polyacrylamide (LPA) to efficiently precipitate and purify nucleic acids extracted from complex environmental and ancient tissue samples in one working step. The LPA method replaces the precipitation step in classic liquid‐phase/organic extraction protocols or can be easily applied as an additional post‐extraction step on impure DNA extracts. As a proof of concept, we experimented with this method on different ancient human mummy samples (bones, soft tissues and gut contents) from different time periods (5000 BC–1800 AD), as well as on complex environmental samples (e.g. soil, activated sludge and animal faeces) known to contain inhibitory compounds.
We demonstrated that LPA precipitates nucleic acids, even in an aqueous ethanol solution without the addition of chaotropic salts, resulting in the recovery of highly pure DNA from all tested samples that displayed inhibition with previously published extraction protocols. Compared to the current, most widely used silica‐based extraction method for ancient and sedimentary DNA, our LPA method resulted in comparable DNA qualities and overall DNA compositions (human endogenous content and microbial diversity).
In conclusion, our LPA method with its high purifying capacity provides an important alternative to the commonly used DNA extraction protocols in the environmental and ancient DNA (aDNA) fields.
مستخلص
استخلاص الحمض النووي من العينات البيئية و الأنسجة القديمة المعقدة غالباً ما يكون يقترن باستخلاص بعض المواد المثبطة التي تجعل إجراء المزيد من التحاليل الجزيئية صعبًا أو مستحيلًا. يحدث هذا الاستخلاص المقترن في كلٍ من بروتوكولات استخلاص الأحماض النووية القائمة على حالة الاستخلاص الصلبة أو حالة الاستخلاص السائلة العضوية. في الوقت الحالي ، يتم التغلب على هذا التثبيط إما بإضافة ألبومين المصل البقري (BSA) إلى التفاعلات الإنزيمية اللاحقة أو بتخفيف مستخلصات الحمض النووي. ولكن إضافة الـBSA تقلل التأثير المثبط لمركبات معينة فقط ، وقد يؤدي التخفيف المفرط إلى تغيير النسب الأصلية للحمض النووي.
في هذه الدراسة ، نقدم طريقة جديدة مبتكرة باستخدام عديد الأكريلاميد الخطي (LPA) لترسيب وتنقية الأحماض النووية المستخرجة من العينات البيئية والأنسجة القديمة المعقدة في خطوة واحدة. تحل طريقة LPA محل خطوة الترسيب في بروتوكولات الاستخلاص التقليدية ‐ سواءً في حالة الاستخلاص الصلبة أو السائلة ‐ أو يمكن تطبيقها بسهولة كخطوة إضافية على مستخلصات الأحماض النووية الغير النقية. ولإثبات هذا المفهوم ، جربنا هذه الطريقة على عينات مومياء بشرية قديمة مختلفة (عظام وأنسجة رخوة ومحتويات معوية) من فترات زمنية مختلفة (5000 ق.م. ‐ 1800 م) ، وعينات بيئية معقدة (عينات تربة و حمأة و براز حيوانات) المعروف باحتوائها على مركبات مثبطة.
تمكنا من إثبات أن مادة الـLPA ترسب الأحماض النووية في محلول الإيثانول المائي دون إضافة أملاح تشوتروبيكية chaotropic ، مما يؤدي إلى الحصول على مستخلصات أحماض نووية نقية للغاية من جميع العينات المختبرة التي أظهرت تثبيطًا باستخدام بروتوكولات الاستخراج المنشورة مسبقًا. مقارنةً بأسلوب الاستخلاص القائم على السيليكا ‐ الأكثر استخدامًا حاليًا للحمض النووي القديم والرسوبي ‐ نتج عن طريقة LPA الخاصة بنا صفات مماثلة وتركيبات شاملة للحمض النووي (من حيث المحتوى الأصلي للحمض النووي البشري والتنوع الميكروبي).
وأخيراً ، تمثل طريقة LPA الخاصة بنا ‐ والتي تتميز بقدرتها العالية على التنقية ‐ بديلاً هامًا لبروتوكولات استخراج الحمض النووي شائعة الاستخدام في المجالات البيئية ومجالات الحمض النووي القديم.
Studying infant diet and feeding practices through stable isotope analysis provides direct insight into the life and health of vulnerable population groups in the past. Although the general diet in ...medieval and early modern Livonia has been reconstructed from written sources, little is known about childhood diet during this tumultuous period of Eastern European history. This study presents a comparative investigation of the staple non-adult diet in urban/rural communities during the 13th-17th centuries AD, with a special focus on feeding practices. We aim to reveal the impact of socio-economic circumstances on early childhood nutrition, which affects the physical development and overall survival of this susceptible population group. Bone collagen samples from 176 individuals between the fetal and the 7-15 age categories from four urban/rural South-Estonian cemeteries were cross-sectionally analyzed via EA-IRMS (Elemental Analysis with Isotope Ratio Mass Spectroscopy) for δ13C and δ15N. Results suggest that South-Estonian children had a staple terrestrial C3 diet integrated with animal proteins. Significant divergences were observed between urban and rural sites and slight variation occurred among rural subgroups, possibly resulting from a wider food choice available in towns, different consumption of C4 foods, and/or secular changes. This study provides the first data regarding infant feeding practices in medieval and early modern Livonia. These practices were similar among the different contexts, indicating comparable cultural traditions in child rearing. Breastfeeding was likely practiced for 1-2 years, with supplementary foods introduced around 1 year of age. The weaning process was probably concluded around the age of 3. The δ13C and δ15N values of older children are comparable to those of the adults from the same sites, indicating their diets became similar after weaning, when they started working and obtained a more mature social status.
Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there ...have been claims of smallpox in Egypt, India, and China dating back millennia 1–4, the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial 4–9. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries 4–6 and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics 1, 2, 10. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.
•Variola virus genome was reconstructed from a 17th century mummified child•The archival strain is basal to all 20th century strains, with same gene degradation•Molecular-clock analyses show that much of variola virus evolution occurred recently
Using ancient DNA sequences of variola virus recovered from the mummified remains of a 17th century child, Duggan et al. reconstruct the evolutionary history of smallpox. With the ancient strain, the genetic diversification of the smallpox virus is found to be more recent than previously supposed and concurrent with the onset of widespread vaccination.
This paper presents the first radiological investigation of a collection of Sicilian mummies held in a crypt beneath the Mother Church of Piraino, Italy. The chamber contains 26 preserved bodies of ...religious dignitaries, either conserved vertically in special wall niches or horizontally on wooden shelves. The majority of bodies are clothed, and transportation outside of the crypt was not feasible. Therefore assessment of the remains via paleoradiological methods appeared to be the most convenient approach to investigate this precious ethno-anthropological heritage. Radiological examination of 23 of these mummies yielded information relating to their funerary treatment and some of the pathological alterations associated with the remains. These included osteoarthritis, diffuse idiopathic skeletal hyperostosis, and neoplasms, as well as any trauma present. These analyses provided insights into mortuary behavior and the osteobiographies of these clerical figures.
This article represents a summary of the author’s past 12 years of research on several mummy sets. As mummy studies expand as a sub-specialty of biological anthropology, it is important to highlight ...the significant contribution that the study of preserved remains can provide to both archaeology and history.
Microscopy of mummified visceral tissue from a Medici family member in Italy identified a potential blood vessel containing erythrocytes. Giemsa staining, atomic force microscopy, and ...immunohistochemistry confirmed Plasmodium falciparum inside those erythrocytes. Our results indicate an ancient Mediterranean presence of P. falciparum, which remains responsible for most malaria deaths in Africa.
Background: A medieval mummy known as the Blessed Antonio (Patrizi) is held in the church of Saints Peter and Paul at Monticiano, Sienna, central Italy.Objectives: The aim of our investigation was to ...complete a biological profile of the subject, as well as to assess the impact of deterioration to the concerned remains.Methods: As a follow-up of our bioanthropological, macroscopic approach, two of the samples taken underwent rehydration, fixation, desiccation, paraffin-embedding, and staining according to standard histological techniques applied to mummified remains.Results: The body was determined to be that of an adult male, who showed some pathological changes such as dental calculus and what is suspected to be hallux valgus. The overall preservation of a skin sample revealed damage caused by a post-mortem infestation of insects, while a second, inner sample was identified as lung tissue, and revealed a case of anthracosis.Conclusions: The Blessed Antonio was an adult male, who had poor dental hygiene and was likely exposed to smoke during his lifetime. Damage observed on the remains indicated that a conservation treatment was desirable for the future preservation of the body.
I this study, we examine human skeletal remains from the church of San Francis of Paola located in the small town of Sant’Angelo di Brolo, in the Italian region of Sicily. The preserved skeletal ...remains were temporarily transferred from their permanent resting place in the crypt for a macroscopic examination and evaluation. Various established methods were used to determine age at death, gender, stature, any evidence of disease(s) as well as the fact that there was a minimum of 15 individuals. The findings were then subdivided into different groups of pathologies and recorded as individual cases. Amongst which, dental issues and cases of trauma were most prevalent. Additional conditions such as joint disease, congenital, metabolic and multifactorial disorders were also identified. The prevalence of dental decay indicates that the group’s diet consisted largely of carbohydrates, and that their oral hygiene was poor. Furthermore, evidence of trauma and poor healing suggested that the town was isolated from the main medical centres of the island. Severe complications of traumas linked with a loss of movement and overall independence, as well as physical pain, must have had a significant impact on the lives of those affected.
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