Molecular Egyptology-aDNAand beyond-2024-final-final.pptx

THE PRESENTATION IS A JOURNEY IN ANCIENT EGYPTIAN HISTORY TO REVEAL HOW MUCH WAS ADDED BY USING DNA TO REVEAL DIFFERENT ASPECTS OF THIS CIVILIZATION.

1. Molecular Egyptology Ekbal Mohamed Abo Hashem (MD) Professor of Clinical Pathology, Mansoura University Mummy aDNA , …and beyond

2. AGENDA : Introduction Paleopathology DNA and mummy kinship analysis DNA and Egyptian ancestry Mummy studies in the era of AI The future : new disciplines

3. Egypt is a promising location for the study of ancient populations. It has a rich and well-documented history, and its geographic location and many interactions with populations from surrounding areas, in Africa, Asia and Europe, make it a dynamic region. Recent advances in the study of ancient DNA present an opportunity to test existing understandings of Egyptian history using ancient genetic data.

4. Egypt has always drawn the interests of historians, archeologists, laymen and scientists. Egypt has been a major hub of the old world, the site of one of the earliest ancient civilizations and a major exit corridor for human beings out of Africa. The aDNA research on Egyptian biological remains has been fueled by their abundance and relatively well-preserved state through artificial mummification, as well as by the advanced next-generation sequencing (NGS) technology. Introduction :

5. Mummies, either natural or embalmed, ancient or modern, are the bodies of once living organisms – human and animals – which are “temporarily immortalized.” These bodies and their associated artifacts (e.g., coffins, shrouds, clothes, ceramic and wooden objects, cosmetics, texts, weapons, games) have attracted generations of people of all ages. Why? Because they represent a visible medium between life and death, past and present, human fallacy and eternity.

6. Independently from the region of the world they originated from, these bodies open a window to their past. Through the application of refined investigation techniques as well as philological studies, scholars are challenged to reconstruct the life habits of the individuals of the past, their health state, the environments in which they lived, their beliefs, and their interactions with other cultures.

7. The recorded history of mummy studies begins with Herodotus’s insightful observations of Egyptian mummification procedures, including socioeconomic distinctions between elaborate and less intricate forms. Such differences were confirmed by Diodorus , writing a few centuries later, and then again by the savant P. C. Rouyer , who traveled with Napoleon to Egypt at the turn of the nineteenth century.

8. The Bonaparte incursion, an enormously unsuccessful military effort, ignited an eighteenth-century simmering interest in Egypt into a remarkable Egyptomania that coursed across museums and lecture halls, eventually leading to professional Egyptology with cultural and biological interest in the mummies as people.

9. New findings are used to create a personal profile of each individual, setting them in their historical, geographical, and social contexts, allowing us to explore particular aspects of life or death in ancient Egypt. Insights into their age, beliefs, and the diseases they suffered from help to remind us that all of the mummies were once living people and that, although they died many hundreds of years ago, they still require special ethical considerations .

10. Whether during transport, handling, storage, or display human remains should always be treated with respect, care, and dignity. Although they undoubtedly further our understanding of past human biology and culture, great care and thought must always be given as to the reasons for – and circumstances of – studying and displaying human remains. Egypt announced the start of the National Project for the Study of Royal Mummies in 2019. A $5 million DNA lab was created at the Egyptian Museum, with funding from the Discovery Channel.

11. MUMMIFICATION

12. Natural mummification: can occur with extreme cold conditions ,example is the Otzi iceman (3350-3105 AD) found at the border between Austria and Italy in 1991. Most commonly ,natural mummification occurred in hot dry climates. About 50 incredibly preserved naturally mummified bodies were excavated in the area of the Fourth Nile Cataract in Nubia (modern Sudan) dating back to the late antique and medieval periods (AD 395-1500), during the rescue campaign preceding the building of the Merowe dam. Mummification can occur by either :

13. The mummies, as well as the skeletal remains, are currently the focus of an extensive program of research that will provide new insights into the past inhabitants of the Fourth Cataract. The textile clothing and soft tissues of the mummified individuals are well preserved, with no apparent attempt of artificial mummification. All have been passively conserved, allowing for the use of a broad range of analytical techniques. The hot dry climate in this area kept the mummies in perfect condition . These mummies are part of a larger collection of over a thousand human remains donated to the British Museum .

14. A woman discovered at a site close to the modern village of et- Tereif (British Museum EA 83133), was buried in a pit covered with slabs. Heated by the sun, this enclosed space might have prompted the process of natural mummification. Wrapped in several layers of textiles made of linen and wool, radiocarbon dating indicate that she died around AD 655–775 . The body shows no evidence of embalming; however, her skin and internal organs are remarkably preserved. CT images show that her brain is intact, as well as the lungs, liver, heart, and other organs, which are desiccated but recognizable.

15. The process of artificial mummification the way the Egyptians did it (which was basically - “gut them and soak them in brine for 70 days, then pickle them in sweet smelling spices and wrap them up in linen and seal them in a box”) permitted “soft tissues” to stay kind of, intact for thousands of years. Soft tissues are better than bone, but even bone can yield good DNA if it hasn’t fossilized, where the bone tissue has been replaced with mineral deposits.

16. Because of their exquisite preservation, mummies will continue to provide materials for studies of ancient DNA that will prove important in studying the phylogeography of human diseases . In addition, the recovery of endoparasites and ectoparasites will illuminate histories of these organisms and their relationship to humans . Dietary and residence studies will continue to benefit from mummified tissue preservation

17. Paleopathology has aided our understanding the overall trends in health and population over time. As a field of study, it has started from the 19th century, beginning with mummy unrollings and identification of chronic diseases of known skeletal manifestation, followed by collection of skulls to suggest biological affinity, to finally form a scientific field of research after 1945 with increased focus on standardized methods and systematic data collection .

18. The rehydrated tissues of mummies subjected to autopsy examination result in the diagnosis of many conditions with a considerable degree of confidence and accuracy. Mummified tissues and bones are studied by light and electron microscopy, chemical analyses, and paleoserology . Microbiological studies have not been useful, as viable pathogens have not been cultured from paleopathologic material, although organisms can be identified histologically, including viruses, using electron microscopy. Material and methods of paleopathologic studies Mummies :

19. The advent of X-ray technology enables the non-destructive examination of mummies, aiding in uncovering information beneath the intricate wrappings. This approach, coupled with autopsies on unwrapped bodies, allows experts from all over the world to unveil Egyptian health issues and medical practices. Analyzing bones offers insights into average height, life expectancy, and even the chronological sequence of Egyptian rulers based on age at death. Additionally, examining the skulls of successive pharaohs hints at familial connections and a number of incredible facts. Despite the passage of millennia, mummies persist as a valuable source of information, providing us with a window into the past  

20. Some of the methods bioarchaeologists use include the study of visible signs of infections and diseases on bones like porosities and new bone formation, arthritis, fractures and breaks, DNA and isotopic analysis , NGS, carbon 14 dating , cavities and abscesses in the teeth reflecting high-carb/high-sugar diets, stunting reflecting childhood malnutrition . ELISA (enzyme linked immunosorbent assay) methodology was also used to detect the presence of circulating anodic antigen (CAA)for schistosomiasis.

21. Since a great number of pathogens and parasites have their main localization in visceral body districts, preserved internal organs from Ancient Egypt can be considered to have significant medical interest. Radiological, histological as well as ancient DNA analysis of embalmed viscera may reasonably yield new information about the actual presence, phenotype and genotype of diseases in ancient times, thus leading to a better understanding of their evolution and historical trends . Analysis of visceral contents: Canopic jars

22. Compared to the high number of publications on mummies, only few approaches aimed at determining diseases in ancient internal organs have been produced.

23. Mycobacterium tuberculosis, a pathogen commonly causing serious infections in human history, is particularly important in mummy research. A series of aDNA analyses provided invaluable scientific information on the evolutionary model of M. tuberculosis as well as the interaction between the ancient bacterial pathogen and its hosts: human beings and animals. Microbiological infections : Mycobacteria

24. Examination of an Egyptian mummy of the New Kingdom found in the tombs of the nobles proved the presence of M. tuberculosis aDNA in the ancient Egypt mummy’s lung. Analysis of samples from ancient Egyptian mummies using spoligotyping for M. tuberculosis complex DNA showed similarity when compared with the international database of spoligotyping signatures, whereby the Mycobacterium of the mummies was revealed to be of M. africanum or M. tuberculosis, but not of M. bovis . TB was expanded in ancient Egypt .

25. It is believed that due to the thick lipid-rich bacterial cell wall and the high guanine– cytosine content of its DNA, mycobacterial aDNA might be more persistent than the surrounding host aDNA within the human remains . Evidence also showed the presence of M. leprae, in a 1500-year old mummy from Dakhla Oasis (fourth–fifth century ad) .Using metagenomic analysis, a recent report could detect and construct a near full genomic sequence of M. leprae organism in a ∼2200-year-old mummy from Abusir . This represents the oldest reported full genomic construct of the M. leprae organism.

26. Other bacteria and viruses. It was suggested that diphtheria, another lethal disease, was present in ancient Egypt. The analysis of the 16S rDNA in the tooth sample of an infant mummy provided an evidence for the presence of the causing organism, Corynebacterium spp. Another study presented molecular evidence of bacteremia by gastrointestinal pathogenic bacteria in an infant Egyptian mummy .

27. The recent metagenomic analysis of >100 Egyptian human remains from two anthropological collections could construct hepatitis B viral genome from a 2000-year-old Egyptian mummy as well as detecting a variety of bacteria related to oral pathology among a number of mummies.

28. The microbiome The study of intestinal microorganisms is not rare in mummy studies. The microbiome in the human intestine has a distinct set of microbial inhabitants such as bacteria, viruses, fungi, and others. Nowadays, the microbiome is known to be integrally linked to the health and disease of mankind. In the earliest days of aDNA research, normal flora of mummy stomach and colon was investigated by PCR amplification . However, cutting-edge techniques (high-throughput sequencing and metagenomics) thereafter have been used for analysis of the microbiome.

29. Archaeoparasitology DNA analyses on parasitological specimens (e.g., coprolites) from mummies provide information pivotal to a comprehensive understanding of changes in the genetic characteristics of many parasite species throughout history. The earliest studies on ancient parasite DNA were reported after successful separation of Ascaris genes by PCR amplification performed on archaeological samples, aDNA analysis has been increasingly utilized for phylogenetic analysis of various parasite species.

30. It is assumed that during the Middle Kingdom (ca. 2100–1800 BCE), the ancient Egyptians may have contracted (Plasmodium falciparum) after settling in the Faiyum Oasis and creating channels of stagnant water. Evidence of Malaria infection in Ancient Egypt : Parasitic infestations:

31. Several molecular studies investigated the presence of malaria parasite in ancient Egyptian remains. P. falciparum was identified in two Egyptian mummies who tested positive for the 134-bp fragment of the chloroquine resistance transporter gene . A study on late 18th dynasty provided the earliest evidence of the presence of P. falciparum in the remains of four mummies (Tutankhamun, Thuya , Yuya and TT320-CCG61065) through the identification of plasmodial Merozoite surface protein1, Subtelomeric variable open reading frame and Apical membrane antigen 1 (AMA1) gene fragments in their extracted DNA samples .

32. Ruffer (1859–1917), the founder of modern palaeopathology ,was the first to describe calcified eggs of Schistosoma haematobium in Egyptian mummies more than 100 years ago. Ruffer found the calcified eggs in the kidneys of 2 mummies of the 20th Dynasty. Later studies found eggs of Schistosoma haematobium in Egyptian mummies, such as the Royal Ontario Museum I mummy (ROM I), where not only eggs but also potential alterations in the hepatic architecture were observed . Schistosomiasis:

33. Scientists conducting the autopsy found schistosomal eggs penetrating the muscular layers of the small and large intestines, the bladder and also infestation of the portal areas combined with signs of early cirrhosis, thus suggesting fibrotic response as a result of an infection by Schistosoma.

34. The description and the determinative signs of the ‘ aAa disease’ ( aAa is described as poison) in the famous Ebers Papyrus , may be matched with schistosomiasis. The recipe for the prescribed cure for aAa -disease includes honey (antibacterial) and the Sams-plant, which is perhaps Anacyclus pyrethrum (pellitory, Spanish chamomile ), a medicinal herb used for its blood cleansing properties).

35. The Manchester Egyptian Mummy Project Currently, the Manchester Project has developed immunocytochemistry as an additional diagnostic tool which has been successfully applied to infected ancient and modern tissues . Proposed DNA studies may also reveal the presence in mummies of the parasite that causes this disease. Was established in 1973 and has developed a multidisciplinary methodology for studying Egyptian mummified remains, and has pioneered the use of virtually nondestructive techniques of investigation, particularly endoscopy .

36. An International Egyptian Mummy Databank Was initiated at Manchester, to collect information about mummies held in collections worldwide . In 1995, the Manchester Mummy Project and Medical Service Corporation International of Arlington, Virginia, USA , began a joint study of the epidemiology of schistosomiasis in ancient and modern Egypt.

37. Data on schistosomiasis in mummies will be compared with information which has been collected about the disease in Egypt today, through the Schistosomiasis Research Project (SRP) . The aims of the project are to use modern laboratory techniques to detect the disease in mummies; to compare this information with the epidemiology of the disease in Egypt today; and to describe the epidemiologic evolution of schistosomiasis within Egypt, over a 5000 year timespan.

38. Recent genetic evidence supports the notion that ancient Egyptians used domesticated cats and implies that taming of the cats occurred prior to or during Predynastic and Early Dynastic Periods .The seroprevalence of T. gondii in contemporary Egyptian cats reached 97%. Consequently, the soil is suspected to be heavily contaminated with oocytes . Toxoplasma DNA was identified in soft tissue biopsies from five embalmed heads, using metagenomic NGS analysis. Toxoplasmosis TOXOPLASMOSIS

39. During the investigation of Nakht , whose intestinal tissue had been sampled, numerous eggs of Taenia spp. were found but they could not be further differentiated into T. solium and T. saginata . The individual has been mummified and the organs were extracted, embalmed and put back into the body’s cavity. The immunohistochemical analysis of a macroscopically visible cystic lesion of the stomach wall demonstrated the presence of T. solium . Cysticercosis

40. During the autopsy of PUM II (Pennsylvania University Mummy), a single egg of helminthic nature was detected in the intestinal tissue. Examination showed that it was the roundworm Ascaris lumbricoides. The larvae of this parasite first infest the intestinal tract, and then migrate through the wall of the intestine to the liver, lungs and in a retrograde manner, via the trachea, again to the intestinal tract. This means that during the larval stage in humans, the parasite could be visible in lung, liver or stomach tissue and therefore, findings in canopic jars would not be surprising. Ascaris

41. Tularemia in Ancient Egypt : A virulent epidemic, similar to bubonic plague or typhus, hit Ancient Egypt in the middle of the Bronze Age .. Documented in medical papyri as well as archaeological findings, and re-echoed in biblical texts, a plague entered Egypt's main harbor, Avaris ,through one of the neighboring ethnic(Hebrews) groups around 1715 BC. As a result, the country was severely weakened at a time when it was already facing serious sociopolitical issues. The Epidemic of Tularemia in Ancient Egypt Affected the Course of World History.

42. Hebrews appeared immune against the etiological agent of the epidemic: Francisella tularensis , the Gram-negative bacterium passed by ticks, and that causes tularemia. Urban dwellers of Avaris , who had a limited contact to animals, were defenseless against the virulent strains, unlike the Hebrews, who lived off sheep and other animals. Attempting to consolidate Egypt's central government in the aftermath of the tularemia epidemic, led to the exodus of the Hebrew community from Egypt at a later time .

43. Caused by the largest human-infecting female nematode, Dracunculus medinensis (‘little dragon of Medina’). The adult female can grow up to about 1 meter in length inside the body of the human host . Dracunculiasis is a debilitating but not fatal disease that man has been fighting for millennia and whose eradication has been considered a noble goal by the WHO but difficult to achieve as it is endemic in critical areas of the world where a radical change in life habits and hygienic practices often clash with wars, tribalism and poverty. Guinea worm disease (GWD), dracunculiasis

44. Some of the earliest known evidence of guinea worm disease comes from the Ebers Papyrus, an ancient Egyptian compilation of medical texts dated to about 1550 BCE. The texts described the process of extracting the worm from the body by winding it around a stick.

45. Using amplification refractory mutation system, it was possible to detect a band at the level of the HbS mutated fragment in DNA samples extracted from the teeth of three predynastic Egyptian mummies (∼3200 bc ), suggesting the diagnosis of sickle cell anemia. Another study, reported a G > A transition in the FGFR3 gene at cDNA position 1138, diagnostic of achondroplasia, in cloned PCR products obtained from a first dynasty mummy (∼3000 bc ). Rare(skeletal dysplasias ) and common(atherosclerosis) noncommunicable diseases were also reported in some ancient Egyptian mummies . Noncommunicable diseases

46. Genetic Predispositions to Diseases HLA class II histocompatibility antigen is a protein encoded by the HLA-DRB1 gene. DRB1 alleles are known to be closely associated with rheumatoid arthritis (RA). DNA analysis of the HLA-DRB1 gene to reveal genetic predisposition to RA has been performed on several mummies. DNA studies of mummies also have proved that atherosclerotic cardiovascular disease (ASCVD) was much more common in ancient populations than expected. They, therefore, searched for genetic risk factors of ASCVD by analysis of related SNPs in genome-wide association studies. In the study, they found multiple SNPs of a major risk locus for coronary heart disease, ischemic stroke, atherosclerosis, and sudden cardiac death

47. The genetic relatedness of individuals from archeological sites has been utilized to elucidate family relationships. Studies on Egyptian human remains assessed the maternal and paternal lineages using both mtDNA sequences and nuclear DNA markers, including autosomal and Y-chromosome short tandem repeats (STRs) . To the best of our knowledge, no full NGS autosomal study has been published yet in this regard, only uniparental markers were utilized. Paleogenomic -Based Kinship Analysis of Ancient Egyptian Human Remains

48. The familial relationships of a number of late 18th dynasty mummies (ca. 1550–1295 b.c. ), including that of Tutankhamen,were demonstrated, based on the analysis of the autosomal and Y-chromosome STR markers in addition to mitochondrial hypervariable region 1 sequences. A 4-generation pedigree of Tutankhamun’s immediate lineage and the identity of his ancestors were established.

49. The Royal male lineage was the Y-chromosome haplogroup R1b that was passed from the grandparent (Amenhotep III) to the father (KV55, Akhenaten) to the grandchild (Tutankhamen). The maternal lineage, the mitochondrial haplogroup K, extended from the great-grandmother ( Thuya ) to the grandmother (KV35 Elder lady, Queen Tiye ) to the yet historically unidentified mother (KV35 Younger lady) to Tutankhamen .

50. Another genetic examination was done as a part of a multidisciplinary study on the mummies of Ramesses III and the Unknown Man E (20th dynasty, circa 1190–1070 bc ). Ramesses III was subjected to an assassination attempt by members of his harem as part of a palace coup, historically known as the Harem conspiracy and recorded in the Judicial Papyrus of Turin. The Unknown Man E was suggested to be Pentaware , the son sharing in the coup. The study concluded, on the basis of radiographic evidence, that the pharaoh was murdered during the attempt. The genetic results confirmed that both mummies had the same Y-chromosome molecular signature, E1b1a haplotype and one set of identical autosomal alleles, suggesting a father–son relationship .

51. In 1980, researchers conducted a number of X-ray examinations on the remains of the New Kingdom of Egypt (1570 – 1050 BC) Pharaohs. The analysis revealed significant resemblances between the rulers of the 19th and 20th Dynasties of the New Kingdom and Mesolithic Nubian samples. They also observed connections to modern Mediterranean populations from the Levant region. This indicated a mixture of ancestry, given the northern origins of the Rammessides   DNA and Egyptian ancestry :

52. EGYPTIAN ANCESTRY

53. X-ray examinations of queen Tiye mummy in 1980 indicated her craniofacial profile aligned with Mesolithic Nubians. DNA results in 2020 unveiled her mtDNA haplogroup K, with Yuya, her father, having Y-DNA G2a and mtDNA K. In 2022, the analysis suggested a genetic affinity with Sub-Saharan Africans among the mummies. However, complexity is noted in biological heritage interpretation. DNA analysis discrepancies among research teams have led to uncertainty about the ancient Egyptians' genetic makeup and origins.

54. Before the emergence of archaeology as a scientific discipline in the late nineteenth century, mummies were perceived as curiosities rather than as sources of important knowledge on ancient societies . Even later, up to the mid-twentieth century, when X-rays began to be used, the investigation of mummies would usually involve their unwrapping, a process that is both irreversible and highly destructive, and little information about mummification was gained . The Emergence of a New Discipline

55. From the 1880s to the early 1900s, the work and publications of Australian anatomist Grafton Elliot Smith (1871–1937), who unwrapped several royal mummies in Cairo, significantly expanded the understanding of the mummification process . Valuable information was also gained from the histological and chemical analysis of mummies – and their embalming materials. Developed in the late nineteenth century, radiology only became widely applied to the study of mummies in the 1960s–70s, when several important collections, including the royal mummies in the Cairo Museum and those in the British Museum, were X-rayed for the first time.

56. This noninvasive approach proved very valuable, revealing a wealth of new information without disturbing the bodies or their wrappings. The unwrapping of mummified remains is now rare and multidisciplinary studies focus on minimally invasive sampling. Extracted from damaged areas or incomplete bodies for histological or chemical analyses, these microscopic samples continue to expand our understanding of ancient diseases and embalming practices.

57. CT Scanning Egyptian Mummies: Data Segmentation and 3D Visualizations Over the last few decades, the use of noninvasive X-ray imaging techniques has transformed the study of mummies. High-resolution three-dimensional (3D) imaging techniques, and in particular Computerized Tomography (CT) scanning, have superseded traditional X-ray machines. A modern CT scanner can analyze an entire body in less than five seconds, generating up to 10,000 two-dimensional X-ray slices (or tomograms) referred to as DICOM (Digital Imaging and Communications in Medicine), with a slice thickness of around 0.3 mm .

58. At the early stage of aDNA analysis, retrieval of aDNA molecules largely depended on polymerase chain reaction (PCR), a technique that was at that time instrumental to the analysis of small amounts of aDNA remnant in archaeological specimens. Due to technical difficulties and low throughput, however, genetic information retrieved by PCR was limited to a small number of loci. DNA and mummy studies

59. Another major issue in the early days of aDNA study was the authenticity of PCR-amplified products. Most importantly, due to the poor preservation status of aDNA fragmented by oxidative or hydrolytic reactions, even a small amount of contamination from modern sources can dominate the PCR products. That is, PCR of targeted sequences might not exclusively amplify authentic aDNA fragments, but also modern exogenous, contaminant DNA.

60. Technical advances during the last decade have provided a major breakthrough in terms of throughput and authenticity in aDNA study. First, next-generation sequencing (NGS) could provide the necessary throughput to enable shotgun sequencing of ancient genomes, even in cases where the amount of exogenous,contaminant DNA far exceeds that of authentic, endogenous aDNA . Prior to the introduction of NGS techniques to aDNA analysis, only short stretches of mtDNA or a few other loci could be acquired from ancient specimens .

61. The novel techniques of DNA capturing that substantially enriches either the whole genome or a predefined set of genomic regions within the sequencing library. By application of capturing techniques, extremely poorly preserved samples can be analyzed . Finally,it is now known that certain skeletal elements (e.g., the otic capsule protecting the inner ear bone) preserve endogenous DNA far better than others . With the advancement of NGS, even ultra-short aDNA fragments (as short as 30–35 base pairs; bps) can now be analyzed by parallel sequencing. This cutting-edge technique thus rapidly replaced conventional PCR commonly used in archaeological science in the past .

62. DNA analysis of archaeological samples has been carried out to obtain forensic DNA profiles of buried individuals using autosomal short tandem repeat (STR) genotyping. DNA fingerprinting techniques have been used for the reconstruction of the family trees of historically important people. DNA analysis was performed on the kindred of Tutankhamun, one of the most famous kings of all ancient civilizations. DNA Fingerprinting Techniques:

63. Genetic fingerprinting allowed the construction of a 5-generation pedigree of Tutankhamun's immediate lineage. The KV55 mummy and KV35YL were identified as the parents of Tutankhamun. No signs of gynecomastia and craniosynostoses ( eg , Antley -Bixler syndrome) or Marfan syndrome were found, but an accumulation of malformations in Tutankhamun's family was evident. Several pathologies including Köhler disease II were diagnosed in Tutankhamun; none alone would have caused death.

64. Genetic testing for STEVOR, AMA1, or MSP1 genes specific for Plasmodium falciparum revealed indications of malaria tropica in 4 mummies, including Tutankhamun’s. These results suggest avascular bone necrosis in conjunction with the malarial infection as the most likely cause of death in Tutankhamun. Walking impairment and malarial disease sustained by Tutankhamun is supported by the discovery of canes and an afterlife pharmacy in his tomb.

65. Whereas there are only two copies of nuclear genomes per diploid cell,hundreds and even thousands of mitochondrial (mt) DNA copies exist in a single cell. Because of this high copy number, mtDNA analysis has been commonly performed in genetic investigations of mummies . In Egypt, mtDNA studies have targeted both human and nonhuman mummies. Their analyses revealed that ancient Egyptians shared an ancestry with the people of the Near East, and that Egyptian mummies could be considered as a repository of ancient genetic data revelatory of past human migration history. Analysis of Mitogenome

66. The metagenomics data could screen bacterial ribosomal RNA (rRNA)-specific reads where they found metagenome sequences of T. denticola aDNA , revealing that disease-associated microorganisms could be detected by metagenomics for datasets from ancient human remains. Although most of the work on ancient nucleic acid has concentrated on DNA, evolutionary conservation of small noncoding micro-RNAs was observed in Ötzi the Iceman. Specific ancient microRNAs in the various 5300-year-old tissue specimens could be obtained . Is another scope that mummy research promises to expand. Metagenomics

67. In an era where technology is revolutionizing our ability to foresee the future, from predicting individual lifespans to deciphering critical climate change thresholds, it’s also proving to be an ally to historians in unraveling the secrets of Egyptology, including Egyptian pharaohs’ lives, deaths, and even their physical appearances. Egyptian mummy studies in the era of AI : UNLOCKING PAST SECRETS

68. computer engineering is using AI to carry out 3-dimensional X-rays of Egyptian mummies. Using artificial intelligence techniques, the tool provides microtomography images of Egyptian mummies. Microtomography works just like a medical scanner, using synchrotron radiation instead of a conventional X-ray source, to capture volumetric scans at much higher resolution and quality ,example: ASEMI (automated segmentation of microtomography imaging). Egyptian Mummies Come to Life with AI Scanner

69. Using the developed software, the human specialist only needs to manually segment a small sample of the volumetric image. This is used to train and automatically optimise a machine learning system, which can then segment the whole volume in a fraction of the time previously required. Following the principles of “Open Innovation, Open Science, Open to the World”, the developed algorithms, data sets, and results have been made freely available to the general public. Meanwhile, for ancient texts, historians are harnessing AI and deep learning to decipher faded writings and identify the origin of these texts.

70. AI facial construction of some famous ancient Egyptian characters Ramsess II Nefertiti King TuT Akhenaton

71. Inspired by mummies’ impressive preservation status, the earliest aDNA studies chose them as the research focus. Since then, DNA research in mummy studies has advanced in parallel with developments in the general field of archaeogenetics. Especially, switching from targeted PCR-based data production to high-throughput NGS of whole metagenomic libraries marked a major qualitative transition in the field. Conclusion:

72. In addition to far higher throughput, NGS has decisive advantages over PCR: it can access, without bias, the ends of aDNA molecules where most of the characteristic chemical damage accumulates, and it offers a statistical approach to the estimation of the level of contamination based only on sequence data . It is anticipated that the research line of molecular Egyptology will be a cornerstone in the coming age of evidence-based archeology.

73. The paleogenomic investigation will definitely help in filling defined gaps of knowledge within the fields of anthropology, archeology, evolution and history, as well as providing paramount information about the coevolution of human host–microbe interrelationship throughout history. Soft tissues, due to their scarcity relative to hard tissues in ancient skeletal remains, generally have comprised only minor fractions of ancient samples yielding genome-scale data in recent large-scale archaeogenetic studies.

74. The genetic study of mummies has a potential to explore subjects that are impossible or extremely difficult to achieve by the genetic study of skeletal remains, such as microbiomes associated with soft tissues (e.g., gut, skin), genetic changes associated with tumors,and the epigenetic makeup of soft tissues. As the history of archaeogenetics to date suggests, laboratory and computational breakthroughs will continually expand the range of information stored in macro biomolecules. We firmly believe that future aDNA research on mummies will continue to evolve and overcome the current limitations.

75. Downloaded from https://academic.oup.com/hmg/article/30/R1/R24/5924364 by guest on 13 October 2023 Human Molecular Genetics, 2021, Vol. 30, No. 2 R27 History of Ancient DNA Analysis in Mummy Research 275 SOURCES : Human Molecular Genetics, 2021, Vol. 30, No. 2 R24–R28 doi : 10.1093/ hmg /ddaa223 Advance Access Publication Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship Yehia Z. Gad1,4,*,†, Naglaa Abu- Mandil Hassan1,5, Dalia M. Mousa1, Fayrouz A. Fouad1, Safaa G. El-Sayed2, Marwa A. Abdelazeem6, Samah M. Mahdy3, Hend Y. Othman1, Dina W. Ibrahim6, Rabab Khairat4,6 and Somaia Ismail4 Noor-Book.com موسوعة مصر القديمة (2) - Copy.rar \ سليم حسن موسوعة مصر القديمة - RAR 4.x archive, unpacked size 281,628,647 bytes

76. 404 | NATURE | VOL 472 | 28 APRIL 2011