Strontium Isotope Signals in Cremated Petrous Portions as Indicator for Childhood Origin

Dental enamel is currently of high informative value in studies concerning childhood origin and human mobility because the strontium isotope ratio in human dental enamel is indicative of geographical origin. However, many prehistoric burials involve cremation and although strontium retains its original biological isotopic composition, even when exposed to very high temperatures, intact dental enamel is rarely preserved in cremated or burned human remains. When preserved, fragments of dental enamel may be difficult to recognize and identify. Finding a substitute material for strontium isotope analysis of burned human remains, reflecting childhood values, is hence of high priority. This is the first study comparing strontium isotope ratios from cremated and non-cremated petrous portions with enamel as indicator for childhood origin. We show how strontium isotope ratios in the otic capsule of the petrous portion of the inner ear are highly correlated with strontium isotope ratios in dental enamel from the same individual, whether inhumed or cremated. This implies that strontium isotope ratios in the petrous bone, which practically always survives cremation, are indicative of childhood origin for human skeletal remains. Hence, the petrous bone is ideal as a substitute material for strontium isotope analysis of burned human remains.     

Fire and bones: Bronze Age III in the North-Eastern Iberian Peninsula

Between the third millennium BP and the fifth century AD, there are numerous necropolises that house urns in the Iberian Peninsula. One example is the "Pi de la Lliura" (Vidreres, Girona). However, there is a dearth of research concerning these structures. The "Pi de la Lliura" housed 43 structures, which contained a total of 47 vessels with human remains. Of these 43 structures, 22 were totally or partially excavated at the laboratory. The evidence from the fragments indicates cremation at a temperature of 650-700 degrees C. Part of the cremated corpse was then deposited in an urn. One of the most unique characteristics of the necropolis is the high frequency of individuals younger than 20 years old. The mortality of sub-adults is high in any prehistoric necropolis, but it is even higher in a cremation necropolis. "Pi de la Lliura" is a very small necropolis, where corpses were treated similarly over a short period.     

Cremation practices and the survival of ancient DNA: burnt bone analyses via RAPD-mediated PCR

Numerous burial rites have been developed in different time periods of human cultural evolution. One of the most interesting burial practices was the ritual cremation of human bodies. Due to the respective cultural and religious background, brand graves are known where human remains had been buried together with burnt bones of animal origin. To date, burnt bone samples have been refractory to PCR-mediated amplification. D/L values of aspartic acid far greater than 80 x 10(-3) were measured in the samples thus indicating the presence of severely nicked and fragmented nucleic acids. In order to differentiate between burial gift of animal origin and burnt human specimens we established a highly sensitive protocol that addresses all the shortcomings connected to degraded ancient DNA. With the novel procedure it was possible to classify 4 specimens ranging from 2,000-5,000 BP on the basis of mitochondrial DNA sequences.     

An approach to funerary rituals in the Roman provinces: plant remains from a Gallo-Roman cemetery at Faulquemont (Moselle, France)

Archaeobotanical studies of funerary offerings allow important insights into beliefs in the afterlife and rituals in the past. Although the number of such investigations has increased in recent years, there are still only a very few systematic investigations of Gallo-Roman cremation graves, especially in northern France. The archaeobotanical study presented here concerns the cemetery (necropolis) of Faulquemont, located in the Département of Moselle. 70 cremation graves, dated from the 1st up to the beginning of the 3rd century A.D. have been sampled for the study of the botanical remains. The graveyard belongs to a rural site. The structures, mainly pits, contained secondary deposits of cremations, characterised by ashy fillings, broken archaeological burned material, bones and carbonised plant remains. 18 plant species have been identified including cereals, pulses, tubers and fruits plus bread/pastry. The most important ones were Triticum (hulled wheat), Hordeum (hulled barley), Lens (lentil) and Pisum (pea). There were also more “exotic” finds like Olea (olive), Phoenix (date) and Lupinus (lupin). The preservation of the cereals suggests possible cooking before cremation, or a long exposure to the fire. Some other plants like hazelnut and olive were maybe consumed as a component of funerary meals. In addition, there were also complete fruits burned as funerary offerings. Only the wealthy deceased received luxurious products such as date. Altogether, the spectrum of Faulquemont fits very well with the known picture of plant offerings during Gallo-Roman times. Electronic Supplementary Material Supplementary material is available for this article at     

From a dry bone to a genetic portrait: a case study of sickle cell anemia

The potential and reliability of DNA analysis for the identification of human remains are demonstrated by the study of a recent bone sample, which represented a documented case of sickle cell anemia. beta-globin gene sequences obtained from the specimen revealed homozygosity for the sickle cell mutation, proving the authenticity of the retrieved residual DNA. Further investigation of mitochondrial and Y chromosome DNA polymorphic markers indicated that this sample came from a male of maternal West African (possibly Yoruban) and paternal Bantu lineages. The medical record, which became available after the DNA analyses had been completed, revealed that it belonged to a Jamaican black male. These findings are consistent with this individual being a descendent of Africans brought to Jamaica during the trans-Atlantic slave trade. This study exemplifies how a "reverse population genetics" approach can be applied to reconstruct a genetic profile from a bone specimen of an unknown individual.     

Cremation--biological source for gender research

This article presents a project designed for prehistoric gender research. It focuses on the late Bronze Age to early Iron Age urnfield in Cottbus "Alvensleben-Kaserne", Brandenburg. The cremation remains were emptied from the urns layer by layer. This provided excellent conditions for a critical reconstruction of the funeral rituals related to the cremation. Detailed recording of each bone fragment in each layer made possible the discovery of the ritual deposition of burnt bones according to the anatomical order. Cremated bones, a primarily biological source, are also a substantial resource for cultural historical research, e.g., on funeral practices as well as social structures.     

Ancient Human Genomes and Environmental DNA from the Cement Attaching 2,000-Year-Old Head Lice Nits

Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.     

Propylene glycol: a promising preservative for insects,comparable to ethanol,from trapping to DNA analysis

Recent advances in DNA analysis allow us to identify an unprecedented number of insect samples collected by mass sampling techniques such as insect traps. In these circumstances, a preservative that can be applied from trap to storage is necessary to prevent degradation of DNA before analysis and save on the cost of labor for collecting insects from traps. Propylene glycol has a prominent feature as a trap solution. We aimed to examine the DNA preservability of 98% propylene glycol at 2 weeks and more than 6 months after initial collection in comparison with 99.5% ethanol, which is commonly used for storage of specimens for genetic analysis. We compared amplification performance of PCR targeting a specific region of the mitochondrial cytochrome c oxidase subunit I (COI) gene in the orders Hymenoptera, Diptera, and Coleoptera using two extraction methods varying in extraction efficiency. Even after 6 months, more than 75% of samples were recognized to have succeeded in PCR amplification irrespective of preservatives by the extraction method with higher extraction efficiency. It suggested that mitochondrial DNA was preserved in both solutions. However, dim bands in the electrophoreses of PCR products increased with time in extracts by another method with lower extraction efficiency. In Diptera and Coleoptera, the rate of dim bands increased more rapidly for ethanol-preserved than for propylene glycol-preserved specimens, indicating higher DNA preservability of propylene glycol over time for these taxa. On the other hand, in Hymenoptera, the preservatives did not affect PCR amplification performance. Considering its safer characteristics and high DNA preservability in a wide range of taxa, propylene glycol can be a promising solution from trapping of insects to storage for genetic analysis.     

Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA

Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis.     

旧石器遗址出土烧骨的技术分析及其对考古学的启示

烧骨常见于各类旧石器时代遗址中,作为用火残留物的一类,烧骨对研究人类用火行为有着极为重要的意义,而目前国内针对烧骨的研究工作开展得尚不够深入。本文通过介绍目前烧骨研究领域中若干种主流的分析手段及其在考古学上的应用,以求能进一步完善国内关于旧石器时代人工用火的研究框架,同时希望能对中国古人类用火能力的相关研究提供有益的借鉴。     

Assessing Phagocytic Clearance of Cell Death in Experimental Stroke by Ligatable Fluorescent Probes

We describe a new histochemical approach for visualization of phagocytic clearance in focal brain ischemia. The approach permits the study of elimination of dead cells in stroke by waste-management phagocytes of any cellular lineage. Although numerous cells of different origins that are capable of phagocytosis are present in ischemic brain, only part of them actively engulf and digest cell corpses. The selective visualization, quantification and analysis of such active phagocytic waste-management are helpful in assessing brain response to ischemia. Efficient cell death clearance is important for brain recovery from ischemic injury, as it opens the way for the subsequent regenerative processes. The failure to clean the corpses would result in a toxic reaction caused by non-degraded DNA and proteins. The described procedure uses fluorescent probes selectively ligated by a viral topoisomerase to characteristic DNA breaks produced in all phagocytes during engulfment and digestion of cells irreversibly damaged by ischemia. The method is a new tool for the investigation of brain reaction to ischemic injury.     

Comparative mitochondrial and nuclear quantitative PCR of historical marine mammal tissue,bone, baleen,and tooth samples

The use of historical and ancient tissue samples for genetic analysis is increasing, with ever greater numbers of samples proving to contain sufficient mitochondrial and even nuclear DNA for multilocus analysis. DNA yield, however, remains highly variable and largely unpredictable based solely on sample morphology or age. Quantification of DNA from historical and degraded samples can greatly improve efficiency of screening DNA extracts prior to attempting sequencing or genotyping, but requires sequence‐specific quantitative polymerase chain reaction (qPCR) based assays to detect such minute quantities of degraded DNA. We present two qPCR assays for marine mammal DNA quantification, and results from analysis of DNA extracted from preserved soft tissues, bone, baleen, and tooth from several cetacean species. These two assays have been shown to amplify DNA from 26 marine mammal species representing 12 families of pinnipeds and cetaceans. Our results indicate that different tissues retain different ratios of mitochondrial to nuclear DNA, and may be more or less suitable for analysis of nuclear loci. Specifically, historical bone and tooth samples average 60‐fold higher ratio of mitochondrial DNA to nuclear DNA than preserved fresh soft tissue, and the ratio is almost 8000‐fold higher in baleen.     

DNA decay rate in papyri and human remains from Egyptian archaeological sites

The writing sheets made with strips from the stem (caulis) of papyri (Cyperus papyrus) are one of the most ingenious products of ancient technology. We extracted DNA from samples of modern papyri varying in age from 0-100 years BP and from ancient specimens from Egypt, with an age-span from 1,300-3,200 years BP. The copy number of the plant chloroplast DNA in the sheets was determined using a competitive PCR system designed on the basis of a short (90 bp) tract of the chloroplast's ribulose bisphosphate carboxylase large subunit (rbcL) gene sequence. The results allowed us to establish that the DNA half-life in papyri is about 19-24 years. This means that the last DNA fragments will vanish within no more than 532-672 years from the sheets being manufactured. In a parallel investigation, we checked the archaeological specimens for the presence of residual DNA and determined the extent of racemization of aspartic (Asp) acid in both modern and ancient specimens, as a previous report (Poinar et al. [1996], Science 272:864-866) showed that racemization of aspartic acid and DNA decay are linked. The results confirmed the complete loss of authentic DNA, even in the less ancient (8th century AD) papyri. On the other hand, when the regression for Asp racemization rates in papyri was compared with that for human and animal remains from Egyptian archaeological sites, it proved, quite surprisingly, that the regressions are virtually identical. Our study provides an indirect argument against the reliability of claims about the recovery of authentic DNA from Egyptian mummies and bone remains.     

Phosphatidylserine exposure in Fas type I cells is mitochondria-dependent

Previous studies have demonstrated that Fas-triggered activation of effector caspases and subsequent nuclear apoptosis either is mitochondria-independent (type I cells) or relies on mitochondrial amplification of the initial stimulus (type II cells). We show herein that Bcl-2 overexpression in a prototypic type I cell line (SKW6.4) promotes mitochondrial generation of ATP and blocks Fas-triggered plasma membrane externalization of phosphatidylserine (PS). Moreover, overexpression of Bcl-2 attenuates macrophage engulfment of Fas-triggered cells. Fas-mediated DNA fragmentation, on the other hand, remains unaffected in SKW6.4-bcl-2 cells. These studies thus demonstrate that PS externalization and clearance of cell corpses are mitochondria-dependent events, and show that these events can be dissociated from other features of the apoptotic program, in Fas type I cells.     

Cremation practices coexisting at the S’Illot des Porros Necropolis during the Second Iron Age in the Balearic Islands (Spain)

The necropolis of S’Illot des Porros, one of the most important prehistoric funerary sites of the Balearic Islands (Spain), was in use from the VIth and Vth century BCE until the Ist century CE. Located in a funerary area which contains two cementeries and one sanctuary, this site is constituted by three funerary chambers named A, B and C, respectively. Investigations on all the human burnt bone remains of the chambers, carried out mainly by the X-ray diffraction and supplemented in some cases by Fourier Transform Infrared spectroscopy pointed to the simultaneous use of inhumation and cremation funerary rites, probably due to existing social differences.In particular, it was argued that the chambers were differentiated, i.e., B was dedicated to inhumations and A to cremations, the cremations found in chamber B very likely being a result of a cleaning-purification of the burial area. Moreover, chamber C, which is the most ancient (IVth century BCE) and with the largest number of inhumed remains, contains the smallest number of remains that were exposed to fire and just in one case it seems possible to attribute a genuine high-temperature cremation.     

Ancient mtDNA haplogroups: a new insight into the genetic history of European populations

In the present work, DNA was extracted from 63 skeletal samples recovered at the Neolithic site of San Juan ante Portam Latinam (SJAPL) (Araba, Basque Country). These samples have proved useful as genetic material for the performance of population studies. To achieve this it was necessary to overcome the methodological problems arising when working with damaged DNA molecules. We succeeded in performing an amplification and restriction analysis of the polymorphisms present in the mtDNA. Ninety seven percent of the samples were classified as belonging to one of the nine mtDNA haplogroups described in Caucasians. This work shows that restriction analysis is a useful methodological tool to perform reliable population genetic analysis on archaeological remains. Tha analysis of ancient and modern haplogroup distribution can shed more light on the genetic evolution of human populations. Moreover, a more exhaustive data on prehistoric populations will allow to build stronger hypothesis on the genetic relationships among human populations.     

Demographic Structure and its implications among two breeding isolates of Mali Tribe from Andra Pradesh,India

In the present work, DNA was extrated from 63 skeletal samples recovered at the Neolithic site of San Juan ante Portam Latinam (SJAPL) (Araba, Basque Country). These samples have proved useful as genetic material for the performance of population studies. To achieve this it was necessary to overcome the methodological problems arising when working with damaged DNA molecules. We succeeded in performing an amplification and restriction analysis of the polymorphisms present in the mtDNA. Ninety seven percent of the samples were classified as belonging to one of the nine mtDNA haplogroups described in Caucasians. This work shows that restriction analysis is a useful methodological tool to perform reliable population genetic analysis on archaeological remains. Tha analysis of ancient and modern haplogroup distribution can shed more light on the genetic evolution of human populations. Moreover, a more exhaustive data on prehistoric populations will allow to build stronger hypothesis on the genetic relationships among human populations.     

Novel acriflavin resistance genes, acrC and acrD, in Escherichia coli K-12.

Acriflavine-resistant mutants were isolated from an acriflavine-sensitive (acrA) strain of Escherichia coli K-12 and then tested for temperature sensitivity of cell division. Genetic analysis characterized two new genetic loci, acrC and acrD. The former was mapped between tonA and proA, and the latter between the origin of genetic transfer of HfrH and serB. acrC and acrD mutants could divide but did not initiate a new round of deoxyribonucleic acid (DNA) replication at 43 degrees C. DNA synthesis of the acrC mutant cells ceased after a period of time following temperature shift-up, and thereafter DNA degradation occurred. However, cell mass continued to increase for a long time at the nonpermissive temperature. On the other hand, DNA synthesis of the acrD mutant cells ceased soon after the shift-up, and the cell mass did not appreciably increase during the prolonged incubation.     

Vitreous humour as a potential DNA source for postmortem human identification

PURPOSE: The aim of this study was the assessment of vitreous humor as a potential DNA for forensic human postmortem identification. MATERIAL AND METHODS: Vitreous humor samples were collected using two alternative approaches from 25 corpses of either sex during autopsies. DNA was extracted by standard organic method. Recovered DNA was quantitiated fluorometrically. AmpFlSTR SGM Plus kit and ABI 310 Genetic Analyzer (Applera) were used to obtain genetic profiles. RESULTS: Different DNA yields were quantitated in vitreous body depending on cause of death and sampling approach. CONCLUSION: Vitreous humor is a potential DNA for forensic human postmortem identification depending on a sampling method used.     

Lysosome biogenesis mediated by vps-18 affects apoptotic cell degradation in Caenorhabditis elegans

Appropriate clearance of apoptotic cells (cell corpses) is an important step of programmed cell death. Although genetic and biochemical studies have identified several genes that regulate the engulfment of cell corpses, how these are degraded after being internalized in engulfing cell remains elusive. Here, we show that VPS-18, the Caenorhabditis elegans homologue of yeast Vps18p, is critical to cell corpse degradation. VPS-18 is expressed and functions in engulfing cells. Deletion of vps-18 leads to significant accumulation of cell corpses that are not degraded properly. Furthermore, vps-18 mutation causes strong defects in the biogenesis of endosomes and lysosomes, thus affecting endosomal/lysosomal protein degradation. Importantly, we demonstrate that phagosomes containing internalized cell corpses are unable to fuse with lysosomes in vps-18 mutants. Our findings thus provide direct evidence for the important role of endosomal/lysosomal degradation in proper clearance of apoptotic cells during programmed cell death.