The identification of malaria in paleopathology-An in-depth assessment of the strategies to detect malaria in ancient remains.

The comprehensive analyses of human remains from various places and time periods, either by immunological or molecular approaches, provide circumstantial evidence that malaria tropica haunted humankind at least since dynastic ancient Egypt. Here we summarize the "actual state-of-the-art" of these bio-molecular investigations and offer a solid basis for the discussion of the paleopathology of malaria in human history.

Reconstructing the life of an unknown (ca. 500 years-old South American Inca) mummy--multidisciplinary study of a Peruvian Inca mummy suggests severe Chagas disease and ritual homicide.

The paleopathological, paleoradiological, histological, molecular and forensic investigation of a female mummy (radiocarbon dated 1451-1642 AD) provides circumstantial evidence for massive skull trauma affecting a young adult female individual shortly before death along with chronic infection by Trypanosoma cruzi (Chagas disease). The mummy (initially assumed to be a German bog body) was localized by stable isotope analysis to South America at/near the Peruvian/Northern Chilean coast line. This is further supported by New World camelid fibers attached to her plaits, typical Inca-type skull deformation and the type of Wormian bone at her occiput. Despite an only small transverse wound of the supraorbital region computed tomography scans show an almost complete destruction of face and frontal skull bones with terrace-like margins, but without evidence for tissue reaction. The type of destruction indicates massive blunt force applied to the center of the face. Stable isotope analysis indicates South American origin: Nitrogen and hydrogen isotope patterns indicate an extraordinarily high marine diet along with C4-plant alimentation which fits best to the coastal area of Pacific South America. A hair strand over the last ten months of her life indicates a shift to a more "terrestric" nutrition pattern suggesting either a move from the coast or a change in her nutrition. Paleoradiology further shows extensive hypertrophy of the heart muscle and a distended large bowel/rectum. Histologically, in the rectum wall massive fibrosis alternates with residual smooth muscle. The latter contains multiple inclusions of small intracellular parasites as confirmed by immunohistochemical and molecular ancient DNA analysis to represent a chronic Trypanosoma cruzi infection. This case shows a unique paleopathological setting with massive blunt force trauma to the skull nurturing the hypothesis of a ritual homicide as previously described in South American mummies in an individual that suffered from severe chronic Chagas disease.

First insights into the metagenome of Egyptian mummies using next-generation sequencing.

We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC-124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a "bacterial fingerprint", discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.

Molecular identification of falciparum malaria and human tuberculosis co-infections in mummies from the Fayum depression (Lower Egypt).

Due to the presence of the lake Quarun and to the particular nature of its irrigation system, it has been speculated that the Fayum, a large depression 80 kilometers south-west of modern Cairo, was exposed to the hazards of malaria in historic times. Similarly, it has been speculated that, in the same area, also human tuberculosis might have been far more widespread in the antiquity than in its recent past. If these hypotheses were confirmed, it would imply that frequent cases of co-infection between the two pathogens might have occurred in ancient populations. To substantiate those speculations, molecular analyses were carried out on sixteen mummified heads recovered from the necropolis of Abusir el Meleq (Fayum) dating from the 3(rd) Intermediate Period (1064-656 BC) to the Roman Period (30 BC-300 AD). Soft tissue biopsies were used for DNA extractions and PCR amplifications using well-suited protocols. A partial 196-bp fragment of Plasmodium falciparum apical membrane antigen 1 gene and a 123-bp fragment of the Mycobacterium tuberculosis complex insertion sequence IS6110 were amplified and sequenced in six and five of the sixteen specimens, respectively. A 100% concordance rates between our sequences and those of P. falciparum and M. tuberculosis complex ones were obtained. Lastly, concomitant PCR amplification of P. falciparum and M. tuberculosis complex DNA specific fragments was obtained in four mummies, three of which are (14)C dated to the Late and Graeco-Roman Periods. Our data confirm that the hydrography of Fayum was extremely conducive to the spread of malaria. They also support the notion that the agricultural boom and dense crowding occurred in this region, especially under the Ptolemies, highly increased the probability for the manifestation and spread of tuberculosis. Here we extend back-wards to ca. 800 BC new evidence for malaria tropica and human tuberculosis co-occurrence in ancient Lower Egypt.

Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study.

OBJECTIVE: To investigate the true character of the harem conspiracy described in the Judicial Papyrus of Turin and determine whether Ramesses III was indeed killed. DESIGN: Anthropological, forensic, radiological, and genetic study of the mummies of Ramesses III and unknown man E, found together and taken from the 20th dynasty of ancient Egypt (circa 1190-1070 BC). RESULTS: Computed tomography scans revealed a deep cut in Ramesses III's throat, probably made by a sharp knife. During the mummification process, a Horus eye amulet was inserted in the wound for healing purposes, and the neck was covered by a collar of thick linen layers. Forensic examination of unknown man E showed compressed skin folds around his neck and a thoracic inflation. Unknown man E also had an unusual mummification procedure. According to genetic analyses, both mummies had identical haplotypes of the Y chromosome and a common male lineage. CONCLUSIONS: This study suggests that Ramesses III was murdered during the harem conspiracy by the cutting of his throat. Unknown man E is a possible candidate as Ramesses III's son Pentawere.

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

Enlightening the past: analytical proof for the use of Pistacia exudates in ancient Egyptian embalming resins.

Mastic, the resinous exudate of the evergreen shrub Pistacia lentiscus, is frequently discussed as one of the ingredients used for embalming in ancient Egypt. We show the identification of mastic in ancient Egyptian embalming resins by an unambiguous assignment of the mastic triterpenoid fingerprint consisting of moronic acid, oleanonic acid, isomasticadienonic and masticadienonic acid through the consolidation of NMR and GC/MS analysis. Differences in the observed triterpenoid fingerprints between mummy specimens suggest that more than one plant species served as the triterpenoid resin source. Analysis of the triterpenoid acids of ancient embalming resin samples in the form of their methyl- and trimethylsilyl esters is compared. In addition we show a simple way to differentiate between residues of mastic from its use as incense during embalming or from direct mastic application in the embalming resin.

Epigenetic alterations by methylation of RASSF1A and DAPK1 promoter sequences in mammary carcinoma detected in extracellular tumor DNA.

Novel strategies for early detection of breast cancer, the most common and second most lethal cancer in women, are urgently needed. Silencing tumor suppressor genes via DNA methylation has established hypermethylation as one of the most frequent molecular alterations that may initiate and drive many types of human neoplasia including breast cancer. Detecting such epigenetic changes in DNA derived not only from tumor tissue, but also from bodily fluids, may be a promising target for the molecular analysis of cancer. In this study we examined serum, a readily accessible bodily fluid known to contain neoplastic DNA, from individuals with breast carcinoma. Using sensitive methylation-specific polymerase chain reaction, we searched for aberrant promoter hypermethylation of two normally nonmethylated genes: RAS association domain family member 1A (RASSF1A) and death-associated protein kinase 1 (DAPK1) in 26 patients with breast cancer, 16 patients with benign breast diseases, and 12 age-matched healthy controls. Hypermethylation of at least one gene was detected in 25/26 (96%) cancer patients, in 7/16 (43%) cases with benign breast diseases, and only 1/12 (8%) control subjects. Furthermore, methylation of both genes was found to be associated with ductal type of breast carcinoma. RASSF1A was hypermethylated in 18/26 cases (69%) and DAPK1 in 23/26 (88%). However, DAPK1 promoter methylation was more pronounced, as 12/23 DAPK1 methylated cases (52%) were strongly methylated (>75%) compared to the weaker methylation of RASSF1A (none of the cases with methylation at the level of >75%). These findings, if confirmed in studies of extended cohorts, may lead to useful clinical application in early diagnosis of breast cancer and better management of the neoplastic disease.

Ancestry and pathology in King Tutankhamun's family.

CONTEXT: The New Kingdom in ancient Egypt, comprising the 18th, 19th, and 20th dynasties, spanned the mid-16th to the early 11th centuries bc. The late 18th dynasty, which included the reigns of pharaohs Akhenaten and Tutankhamun, was an extraordinary time. The identification of a number of royal mummies from this era, the exact relationships between some members of the royal family, and possible illnesses and causes of death have been matters of debate. OBJECTIVES: To introduce a new approach to molecular and medical Egyptology, to determine familial relationships among 11 royal mummies of the New Kingdom, and to search for pathological features attributable to possible murder, consanguinity, inherited disorders, and infectious diseases. DESIGN: From September 2007 to October 2009, royal mummies underwent detailed anthropological, radiological, and genetic studies as part of the King Tutankhamun Family Project. Mummies distinct from Tutankhamun's immediate lineage served as the genetic and morphological reference. To authenticate DNA results, analytical steps were repeated and independently replicated in a second ancient DNA laboratory staffed by a separate group of personnel. Eleven royal mummies dating from circa 1410-1324 bc and suspected of being kindred of Tutankhamun and 5 royal mummies dating to an earlier period, circa 1550-1479 bc, were examined. MAIN OUTCOME MEASURES: Microsatellite-based haplotypes in the mummies, generational segregation of alleles within possible pedigree variants, and correlation of identified diseases with individual age, archeological evidence, and the written historical record. RESULTS: 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. 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. CONCLUSION: Using a multidisciplinary scientific approach, we showed the feasibility of gathering data on Pharaonic kinship and diseases and speculated about individual causes of death.

A decade in search of myopia genes.

Nearly half of visual impairment in the world is caused by uncorrected refractive errors, and myopia constitutes a significant proportion of this problem. Moreover, the prevalence of myopia is increasing, especially in Asian countries. Linkage studies have identified at least 18 possible loci (MYP) in 15 different chromosomes associated with myopia, although some of these remain to be confirmed. However, when studies have been carried out to identify specific candidate genes, it is apparent that these genes are often not part of MYP loci. In studying the expression of specific genes that might be responsible for myopia, we are learning that the involvement of various small leucine-rich repeat proteoglycans and growth factors is not a simple one. The emerging picture is one of complex interaction, in which mutations in several genes likely act in concert. The majority of myopia cases are not likely caused by defects in structural proteins, but in defects involving the control of structural proteins. The future of genetic research in this area will likely rely increasingly on microchip array technology.

Otoferlin interacts with myosin VI: implications for maintenance of the basolateral synaptic structure of the inner hair cell.

Otoferlin has been proposed to be the Ca(2+) sensor in hair cell exocytosis, compensating for the classical synaptic fusion proteins synaptotagmin-1 and synaptotagmin-2. In the present study, yeast two-hybrid assays reveal myosin VI as a novel otoferlin binding partner. Co-immunoprecipitation assay and co-expression suggest an interaction of both proteins within the basolateral part of inner hair cells (IHCs). Comparison of otoferlin mutants and myosin VI mutant mice indicates non-complementary and complementary roles of myosin VI and otoferlin for synaptic maturation: (i) IHCs from otoferlin mutant mice exhibited a decoupling of CtBP2/RIBEYE and Ca(V)1.3 and severe reduction of exocytosis. (ii) Myosin VI mutant IHCs failed to transport BK channels to the membrane of the apical cell regions, and the exocytotic Ca(2+) efficiency did not mature. (iii) Otoferlin and myosin VI mutant IHCs showed a reduced basolateral synaptic surface area and altered active zone topography. Membrane infoldings in otoferlin mutant IHCs indicated disturbed transport of endocytotic membranes and link the above morphological changes to a complementary role of otoferlin and myosin VI in transport of intracellular compartments to the basolateral IHC membrane.

Fronto-ethmoidal encephalocele in a historical skull with artificial deformation and no signs of chronic elevated intracranial pressure.

The intentional deformation of human skulls in the living being was one of the most curious rituals performed in historical and ancient times. It is thought that these practices cause chronic elevated intracranial pressure and subsequent symptoms of cognitive impairment. In this report, we examine such an artificially deformed skull dating from the sixteenth century that in addition shows a fronto-ethmoidal encephalocele. However, although the mild encephalocele was already manifest at birth and deformation practices were performed over years, the encephalocele did not progress into a more severe status. We conclude that the intentional deformation of skulls does not lead to chronic elevated intracranial pressure and mental retardation.

Rab8b GTPase, a protein transport regulator, is an interacting partner of otoferlin, defective in a human autosomal recessive deafness form.

Mutations within OTOF encoding otoferlin lead to a recessive disorder called DFNB9. Several studies have indicated otoferlin's association with ribbon synapses of cochlear sensory hair cells, as well as data showing the protein's presence in neurons, nerve fibers and hair cells, suggesting a more ubiquitous function. Otoferlin's co-localization not only with ribbon synaptic proteins, but also with additional endosomal (EEA1) or Golgi proteins (GM130) were motivation for a search for further binding partners of otoferlin by a yeast two-hybrid screen in a rodent cochlear cDNA library (P3-P15). This screen identified Rab8b GTPase as a novel interacting partner, substantiated by transient co-expression and co-localization in HEK 293 cells and co-immunoprecipitation of the complex using tagged proteins in vitro and native proteins from cochlea. This finding implies that otoferlin could be a part of components contributing to trans-Golgi trafficking.

Lack of Tff3 peptide results in hearing impairment and accelerated presbyacusis.

Tff peptides are secreted mainly by the gastrointestinal epithelial cells and their primary role is maintaining normal structure and function of mucous epithelia. Ongoing studies on their expression pattern have disclosed other sites of their synthesis thus revealing additional physiological functions in the organism. Here we present new data about Tff3 expression in the cochlea of the rodent inner ear. On the basis of RT-PCR we describe the presence of Tff3 transcripts in both, a mouse cDNA library isolated from whole cochleae from postnatal days 3-15 (P3-P15), and also in cochlear tissue. By using a riboprobe for the fragment containing exon 1, 2 and 3 of Tff3, in situ hybridization, localized Tff3 signals in neurons of spiral ganglion and vestibular organ. We did not observe any abnormalities in the middle ear of Tff3 knock-out mice, neither did histological examination of the inner ear indicate any gross morphological changes in the cochlea. However, ABR (auditory evoked brain stem responses) audiograms revealed that the Tff3 knock-out animals show an accelerated presbyacusis and a hearing loss of about 15 dB at low frequencies increasing to 25 dB loss at higher frequencies. These findings suggest that Tff3 could play a role in neurosensory signaling. Further studies are needed to clarify this new function in the auditory system.

Refinement of the MYP3 locus on human chromosome 12 in a German family with Mendelian autosomal dominant high-grade myopia by SNP array mapping.

Myopia, or short-sightedness, is the most common form of vision disorder worldwide. Higher levels of myopia, usually defined as an axial eye length of >26 mm or a refractive error of < -5.00 diopters are often designated as 'pathologic' myopia, because of the predisposition to develop further eye disorders such as retinal detachment, macular degeneration, cataract, or glaucoma. Many distinct forms of autosomal dominant non-syndromic high-grade myopia are described in humans. While the underlying chromosomal locations and critical disease intervals have been identified and located to physical map positions, the gene defects and causative mutations responsible for autosomal dominant myopia remain elusive to date. Examination of a German six-generation kindred by 10K whole genome chips led to the identification of a 19-cM map segment as being the most likely familial myopia candidate region spanning from chromosomal band 12q14.3 to 12q21.31 (MYP3). In our family, a maximum multi-point LOD score of 3.9 was obtained between rs1373877 and rs717996. The recombination breakpoints in this family and the interval of the originally reported German/Italian family defining the MYP3 locus on chromosome 12 (OMIM 603221, two-point LOD score 3.85 for markers D12S1706 and D12S327 at 12q21-23) allowed us to significantly refine a minimum consensus region. This new composite region is located between microsatellite marker D12S1684 at 75.8 K and SNP_A-1509586 (alias rs717996) at position 82,636,288 bp, and narrows the original 30.1 cM of the MYP3 interval to 6.8 cM. The refined MYP3 interval allowed us to restrict the list of database-indexed genes to 25, several of which are promising MYP3 candidates based on similarities with genes and proteins involved in vision physiology and eye disease. While autosomal dominant high-grade myopia is recognized to be genetically heterogeneous, our results suggest genetic homogeneity of the MYP3-based condition in families that share the same ethnic and geographical background. The future identification of this MYP3 gene may provide insights into the pathophysiology of myopia and eye development.

Cytokine regulation of the trefoil factor family binding protein GKN2 (GDDR/TFIZ1/blottin) in human gastrointestinal epithelial cells.

Trefoil factor family (TFF) peptides are major secretory products of mucous epithelia and play a multifunctional role in cytoprotection, apoptosis, and immune response. Recently, a TFF2-binding protein was discovered in mice and named blottin. It is down-regulated in gastric cancer (GDDR), abundant in human gastric surface (TFIZ1) and its similarity to gastrokine-1 led to the gene's name GKN2. To investigate the mode of GKN2 regulation activity of a luciferase reporter gene, controlled by the GKN2 promoter, was monitored upon treatment with various pro-inflammatory (TNF-alpha, IL-1beta, IL-6, IFN-gamma) and anti-inflammatory (TGF-beta1) cytokines using gastric (AGS, KATO III) and colonic (HT-29) cell lines. To assess the direct role of transcription factors (NFkappaB, HNF-3beta, hGATA6) in regulating GKN2 we performed transient co-transfection of their expression plasmids and the reporter gene construct. GKN2 gene was down-regulated by pro-inflammatory cytokines in all tested cell lines while up-regulated by TGF-beta1 only in the colonic cell line. GKN2 expression was significantly reduced in both gastric adenocarcinoma cell lines by the active form of NFkappaB transcription factor, whereas in the colonic cell line an up-regulation was noticed. Down-regulation by IL-6 was mediated by C/EBPbeta transcription factor in case of HT-29 but not of KATO III cells. We conclude that the regulation of GKN2 parallels that of TFF genes, indicating that together they may play an important role in maintaining the homeostasis of the gastrointestinal tract.

Population haplotypes of exon ORF15 of the retinitis pigmentosa GTPase regulator gene in Germany : implications for screening for inherited retinal disorders.

BACKGROUND: Mutations in exon ORF15 of the retinitis pigmentosa GTPase regulator gene (RPGR) within chromosomal region Xp21.1 are a significant cause of a number of retinal disorders. The high mutation rate is ascribed to the highly repetitive, purine-rich tracts within the exon ORF15 sequence. Importantly, all exon ORF15 mutations observed to date represent protein-truncating mutations (nonsense and frameshift mutations). Because of its repetitive motifs, mutation screening of the hot-spot region by direct DNA sequencing is a technically challenging task. METHODS: We devised a screening strategy for exon ORF15 mutations that reserves DNA sequencing for precise sizing and base-order assessment of detected mutations. The screening strategy is based on a PCR/restriction fragment length polymorphism (RFLP) analysis of exon ORF15 and comparison with population-specific RFLP haplotypes. The latter were constructed from PCR/RFLP analysis of DNA samples from 100 healthy German male individuals. Mutational alterations of normal RFLP haplotype patterns were predicted. RESULTS: Six distinct RFLP haplotypes (founder alleles H1-H6) were observed with frequencies ranging from 2% to 63%. All natural variations of exon ORF15 were in-frame alterations ranging in size between 3bp and 36bp. Prediction of mutation-specific RFLP patterns indicated a high detection rate of mutations. CONCLUSION: A new strategy has been developed using routine protocols for mutation screening of difficult-to-sequence, highly repetitive exon ORF15 of the RPGR gene in a German population.

Mutational risk in highly repetitive exon ORF15 of the RPGR multidisease gene is not associated with haplotype background.

Exon ORF15 is an alternative exon in the retinitis pigmentosa GTPase regulator (RPGR) gene containing a highly repetitive, purine-rich internal region. It constitutes a mutational hot spot giving rise to a group of heterogeneous X-linked retinal disorders. We sought to determine whether non-pathogenic substitutions and sequence length variations in the repetitive sequence have an influence on the risk of pathogenic exon ORF15 mutations. The type and distribution of exon ORF15 polymorphisms were assessed by genotyping 107 healthy German males using standard procedures. Polymorphisms were grouped into haplotypes and their frequencies determined in normal controls and previously analyzed patients with X-linked retinitis pigmentosa (XLRP). In the control group we identified 6 complex variants of the most common, ancestral exon ORF15 allele corresponding to the GenBank reference sequence (accession no. AF286472). Exon ORF15 mutations in XLRP patients were associated with the ancestral allele in 75% of affected cases. Four of the most recent founder haplotypes termed H3, H4, H6 and H7 were not identified in the patient samples. Our analysis and review of polymorphism data from the published literature suggests the presence of common exon ORF15 haplotypes in the European population. While the mutational risk in the RPGR gene appears not to be altered by the haplotype background, exon ORF15 haplotype analysis may be useful for tracing the evolutionary history of RP3-associated diseases.