Analysis of ancient mycolic acids by using MALDI TOF MS: response to “Essentials in the use of mycolic acid biomarkers for tuberculosis detection” by Minnikin et al., 2010

The mycobacterial cell wall is consists of several long chain lipid and glycolipid components. Mycolic acids are major and unique fraction of the cell envelope of mycobacteria that include the ancient causative agents of tuberculosis and leprosy. The analytical investigation of these lipid biomarker residues is one of the most promising perspectives in the field of molecular paleopathology. Recently published in this journal, Minnikin et al. present a systematic critique of the MALDI TOF MS analysis for determination of ancient mycolic acids, focusing on our previous paper. In this study, our mass spectrometric investigations by commonly used 2,5 DHB matrix were presented with our comments to the critique authors. On the base of our previous and recent mass spectrometric results we have to realize that the clinical protocols and standards cannot directly be used for the biomolecular paleopathological investigations. The applicability of the recent mycobacterial and clinical results is very limited in the biomolecular archaeology, thus the recent scientific results and protocols should be adapted carefully to bioarchaeological sciences.     

High-throughput mass spectrometric analysis of 1400-year-old mycolic acids as biomarkers for ancient tuberculosis infection

The cell wall of mycobacteria includes an unusual outer membrane of extremely low permeability. This cell envelope consists of a characteristic cell wall skeleton, a mycoloyl arabinogalactan peptidoglycan complex, and related hydrophobic components that contribute to the cell surface properties. In this study 1400-year-old mycolic acids as unique tuberculosis biomarkers have been extracted and identified for the first time by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) and Fourier transform infrared spectroscopy (FT-IR). The data suggest that the MALDI TOF MS has potential as a rapid and reproducible technique for the detection and identification of ancient mycobacterial infections.     

Essentials in the use of mycolic acid biomarkers for tuberculosis detection: response to “High-throughput mass spectrometric analysis of 1400-year-old mycolic acids as biomarkers for ancient tuberculosis infection” by

High molecular weight long-chain mycolic acids are key structural components of the cell envelope of Mycobacterium tuberculosis and they are established as biomarkers for the identification of both ancient and modern tuberculosis. Mycolic acids from M. tuberculosis have a characteristic profile, reflecting contributions from five major distinct homologous series of mycolate structural types. Diagnosis of tuberculosis in archaeological material, using mycolic acid biomarkers, depends on objective recognition of the key characteristic mycolic acid components. A recent article in this journal claimed that tuberculosis could be confirmed in ancient bones by high throughput mass spectrometric analysis of mycolic acids. Scrutiny of the data presented reveals no convincing evidence for the presence of mycolic acids, characteristic of the M. tuberculosis complex, in the skeletal remains examined. This communication reviews the essential criteria necessary for positive tuberculosis diagnosis, using mycolic acids.     

Deficiencies and challenges in the study of ancient tuberculosis DNA

We explore the standards of research and reporting needed to justify the destructive analysis of archaeological human bone for biomolecular studies of ancient tuberculosis (TB). Acceptable standards in osteological interpretation have been met in some biomolecular papers, but there are also cases where insufficient care has been taken in distinguishing between pathognomonic lesions and those that are ‘consistent with’ a diagnosis of TB. Some biomolecular studies have failed to recognize that archaeological bones might be contaminated with environmental mycobacteria whose DNA could give rise to false positives in polymerase chain reactions directed at members of the Mycobacterium tuberculosis complex. The difficulties of applying spoligotyping to ancient DNA have also been underestimated and conclusions drawn from such analyses are often weakly supported. Assumptions that mycobacterial DNA preserves better than human DNA, and that contamination with modern DNA is less of a problem, has led in some cases to a laxity in research standards with insufficient attention paid to the need to authenticate ancient DNA results. We illustrate our concerns by reference to a recent paper reporting biomolecular detection of ancient TB DNA in skeletons from the eastern Mediterranean Neolithic settlement of Atlit-Yam. We are unconvinced that the skeletal evidence presented in this paper gives sufficient indication of TB to warrant destructive analysis, and we are concerned that during the biomolecular part of the project inadequate attention was paid to the possibility that results might be due to laboratory cross-contamination or to amplification of environmental mycobacterial DNA present in the bones.     

Biomolecular archaeology of ancient tuberculosis: response to “Deficiencies and challenges in the study of ancient tuberculosis DNA” by Wilbur et al. (2009)

It is sixteen years since the first detection of Mycobacterium tuberculosis DNA in archaeological specimens, yet the validity of findings continues to be questioned. Rigorous scientific scrutiny and debate is valuable and has led to a coalescence of procedures and precautions amongst those actively engaged in this work. It is disappointing that these good practices are not recognised by certain scientists whose primary expertise is in the related fields of archaeology, palaeopathology, and eukaryote ancient DNA. There is a danger that by constant repetition, disputable and inadequately justified concerns will assume the status of self-perpetuating myths and misunderstandings. We discuss these issues with reference to a recent article in this journal, in which clear peer-reviewed scientific data were specifically targeted as part of a general critique of the field of the palaeomicrobiology of tuberculosis. We believe we have given sufficient evidence and cogent argument to persuade the unbiased reader that the views in the critique by Wilbur et al. are unjustified.     

Identification of psychoactive alkaloids in ancient Andean human hair by gas chromatography/mass spectrometry

Various ethnographic sources have demonstrated the symbolic and ritualistic importance of psychoactive plants in Native American societies. The social milieu of these mind- altering plants appears to be ancient. Archaeological evidence during the Tiwanaku empire expansion along the Atacama Desert of Chile, circa 500–1000 A.D., shows the presence of highly decorated snuffing tablets and tubes as grave goods. The preservation of mummified human bodies in the Azapa Valley, northern Chile, provided an opportunity to test the exact nature of the psychoactive plants used in this region. Using gas chromatography/mass spectrometry (GC–MS), here we show that ancient Andean populations from northern Chile consumed Banisteriopsis, a vine that contains harmine. This is the first direct archaeological evidence of hallucinogenic and medicinal ethnographic practices. Interestingly enough, this rainforest plant does not grow along the Atacama coast, thus our findings suggest extensive plant trade networks in antiquity as far as the Amazon.     

Tikal timbers and temples: ancient Maya agroforestry and the end of time

Tikal, a major lowland Maya civic-ceremonial center in the heart of the Petén region of Central America, relied heavily on the adjacent lowland rainforest as a resource base for fuel and construction materials. In this study, we analyzed 135 wood samples from timbers used in the construction of all six of the city's major temples as well as two major palaces to determine which tree species were being exploited and to better understand ancient Maya agroforestry practices during the Late Classic period. We found evidence for a change in preference from the large-growing, upland forest species, Manilkara zapota, to a seasonal wetland species Haematoxylon campechianum in A.D. 741 as well as a decrease in lintel beam widths over time. Though M. zapota later returned as the wood species of choice in A.D. 810, beam widths were found to be significantly smaller. These findings concur with models that hypothesize widespread deforestation during the Late Classic period and indicate a declining forest resource base by the 9th century A.D. Because of the many large timbers available for temple construction in the 8th century, some system of forest conservation is indicated for the ancient Maya prior to the Late Classic period.     

The persistence of caffeine in experimentally produced black drink residues

Black drink is a native North American caffeinated tea produced from the leaves of Ilex vomitoria. The beverage was an important part of prehistoric Southeastern culture, as it was the only native source of caffeine in North America. The leaves of I. vomitoria were, therefore, a potentially valuable trade resource during the period. As such, the ability to identify archaeological black drink residues is useful to Southeastern archaeologists. In order to determine the plausibility of detecting I. vomitoria in residues, black drink was repeatedly produced in experimental unglazed pottery. The resulting potsherds were buried in several environmental contexts, recovered, and underwent absorbed pottery residue analysis. After two months of burial in three different soil types, plus a control stored in the freezer, caffeine was well-preserved in all sherds, suggesting that caffeine is a potentially useful biomarker for the detection of black drink.     

Treponematosis in Pre-Columbian Jamaica: a biocultural approach to the human cranium found in Bull Savannah

The first inhabitants of Jamaica are now generally referred to as Taínos. It is likely that they arrived in the island after about 650 AD and were extinct by the end of the 16th century. In 1968, during the exploration of a small cave in Bull Savannah, St. Elizabeth parish, Dr. James Lee found two skulls, teeth, bones, and pottery. The aim of this work is to interpret in a biocultural perspective the one cranium with pathological lesions, such as caries sicca. This adult individual had an artificially modified cranium, a cultural practice common among Taínos, which was studied macroscopically and by radiological and computerized tomography. The radiocarbon dates, obtained by AMS, point to the 10th–11th centuries AD and the stable isotopes analysis revealed either the ingestion of a mixed C3/C4 plant diet or an extensive intake of marine resources, the former being more likely. This is the first cranium to be found in Jamaica with evidence of Pre-Columbian treponematosis, most probably syphilis, which has also been demonstrated in a few cases elsewhere in the Caribbean region. This finding agrees with the ethnohistorical narrative, according to which syphilis existed among the native population, who used plant extracts to treat the disease. This paper contributes to our knowledge about the Taínos and the history of treponematosis in the Americas.     

First dendroarchaeological dates of prehistoric contexts in South America: chullpas in the Central Andes

Despite the existence of long-lived tree species with excellent tree-ring characteristics, the use of dendrochronological techniques for dating archaeological contexts has been very limited in South America. Recent research in the Bolivian Altiplano of the Central Andes has yielded a network of Polylepis tarapacana chronologies that goes back to the 13th century. This species was regularly used by local populations since pre-Columbian times as raw material for beams, lintels, hooks and other architectural features in houses, storage chambers, and sepulchers. The aim of this study is to argue in favor of the potential of P. tarapacana for providing high resolution dates of significant archaeological events during the pre-Columbian era. The chronology of chullpas (burial towers and storage chambers) in the southern Andean Altiplano is used as a case study. Growth rings from P. tarapacana have provided several centennial-length dendrochronological records including a reference regional chronology covering the last 786 years in the Central Andean highlands. Based on this long reference chronology calendar years were assigned to woody pieces from pre-Hispanic chullpas. Dendroarchaeological results are consistent with contextual evidence and most radiocarbon dates from woody samples and related archaeological items. Our results indicate that P. tarapacana has a high potential for providing annually-resolved tree-ring dates for archaeological contexts in the Altiplano since the early 13th century.     

Mapping ancient chinampa landscapes in the Basin of Mexico: a remote sensing and GIS approach

This paper uses remote sensing data to document a raised field, chinampa system adjacent to the Postclassic kingdom of Xaltocan in the northern Basin of Mexico. Various forms of landscape information; historic records and maps as well as remote sensing; are considered to understand the chinampa system. The remote sensing data examined include 1950s aerial photographs, Landsat 7 data, and Quickbird VHR, multi-spectral imagery. This article evaluates the utility of each of these forms of data to identify buried chinampa features and integrates them in a GIS to produce a map of Xaltocan's chinampa landscape. Canals of various sizes and hydrological positions comprised the chinampas and integrated the system together. Occupying at least 1500–2000 ha, Xaltocan's chinampa system represents the largest pre-Aztec, chinampa system in the Basin of Mexico.     

Early cat taming in Egypt: a correction

A cat skeleton from a Predynastic burial in Egypt that was previously labelled as Felis silvestris is re-identified as Felis chaus. This means that the previous claim needs to be withdrawn that the specimen represents early evidence for taming of Felis silvestris that ultimately led to domestication. However, the statement that the small felid has been held in captivity for several weeks, based on the presence of healed fractures, is still valid.     

Metals,microanalysis and meaning: a study of metal objects excavated from the indigenous cemetery of El Chorro de Maíta,Cuba

This is the first publication reporting systematic analytical research conducted on archaeological metals from Cuba. The main focus of the study consists of beads and small metal objects excavated at the cemetery of El Chorro de Maíta, which comprises some of the richest funerary deposits so far recovered on the island. Some comparative samples from the nearby site of Alcalá were also investigated, with an emphasis made on the manufacture, composition and origins of the different alloys. The resulting picture is that members of the social elite of the indigenous Taíno peoples were buried with beads made of placer gold exploited locally, gold–copper–silver pendants brought from continental South America and, above all, brass lacetags from European clothing that were perceived as sacred metals. The archaeometallurgical approach offers fresh insight into the relationships between Europeans and Taínos, and the impact of colonization on the indigenous customs, values and social structures.     

Oaks,tree-rings and wooden cultural heritage: a review of the main characteristics and applications of oak dendrochronology in Europe

We overview the recent development of oak dendrochronology in Europe related to archaeology and art-history. Tree-ring series of European oaks (Quercus robur and Q. petraea) have provided a reliable framework for chronometric dating and reconstruction of past climate and environment. To date, long oak chronologies cover almost the entire Holocene, up to 8480 BC and the network over the entire area in which the two oaks grow is being improved. We present the main characteristics of oak ring series and discuss the latest methodological advances in defining the calendar year in which the tree-rings were formed and in interpreting such dating in terms of the age of a wooden object. Dendrochronology has established itself as a standard dating tool and has been applied in a wide variety of (pre-)historical studies. Archaeological wood, historical buildings, works of art (such as panel paintings and sculptures) have been successfully investigated. Recent advances in dendro-provenancing have helped to obtain more information on the timber trade in the past. Information on past forest structures, silviculture and timber use have become available through scrutinizing historical and contemporary ring-width patterns.     

Fishing ancient Lake Baikal,Siberia: inferences from the reconstruction of harvested perch (Perca fluviatilis) size

Fishing was the foundation for many of the world's foraging peoples and was undertaken using a variety of technologies. Reconstructing fishing technologies can be difficult because these tools were often made of perishable materials. Here we explore fishing technologies employed at the Ityrkhei site on Lake Baikal, Siberia. Specifically, we employ regression analyses to reconstruct the sizes of perch (Perca fluviatilis) captured through time at the site. Our analyses demonstrate that almost no juvenile perch were taken, suggesting some selectivity in harvest. We suggest this selectivity is most consistent with the use of relatively large gauge nets or traps. Such mass harvesting technologies may have been important elements of the subsistence economies of Lake Baikal's foraging peoples throughout much of the Holocene.     

Characterization of prehispanic cosmetics found in a burial of the ancient city of Teotihuacan (Mexico)

The present paper reports the chemical data obtained on samples of pigmenting materials contained in 31 miniature vessels found in a burial found in Teopancazco, a multiethnic neighborhood center located in the southeastern sector of the archaeological site of Teotihuacan (Central Mexico) and the analytical protocol established for the complete characterization of these archaeological materials. For this purpose a multi-technique approach based on the combination of several non destructive and micro-destructive instrumental techniques, namely, light microscopy (LM), scanning electron microscopy-X-ray microanalysis (SEM-EDX), transmission electron microscopy (TEM), voltammetry of microparticles (VMP), X-ray microdiffraction (μXRD), X-ray diffraction (XRD), UV-Vis spectrophotometry, FTIR spectroscopy and gas chromatography-mass spectrometry (GC-MS) has been developed in an attempt to completely characterize these materials. These instrumental techniques provide reliable and complementary data including elemental and mineralogical composition, identification of functional groups as well as speciation studies of electroactive species. Among the most relevant findings, volcanic pyroclastic rocks and clayey soils, most probably, from the Teotihuacan valley as well as galena, jarosite and mica from other provenances in Mesoamerica, have been identified. Charcoal and Ocote resin have also been identified. The chemical composition of the samples is discussed with a view to the possible function as cosmetic materials and their use in funerary rites. The results have been critically compared with those others obtained in other ancient civilizations. The study carried out on the materials found in the burial 105 is especially relevant insofar it represents the first evidence, scientifically characterized, of the use of cosmetics in Mesoamerica at this early period (AD 200-550).     

Selective reburial: a potential approach for the in situ preservation of waterlogged archaeological wood in wetland excavations

Excavations at Dispilio, a prehistoric lakeside settlement in northern Greece, have revealed a significant number of vertical wooden piles that need to be protected during and after excavation. Lifting of the piles is not possible and approaches such as reburial, cannot currently be implemented as excavation is still in progress. In 2005, several posts were “selectively buried” on an experimental basis, by encasing them in PVC pipes and backfilling with the surrounding sediment. This approach appeared to be capable of protecting the piles during excavation and be a potential solution for their post-excavation preservation. This preliminary study sets out to asses if this alternative approach to reburial could be an effective in situ preservation method.     

The use of multiple discriminant analysis in classifying prehistoric phytolith assemblages recovered from cooking residues

In the investigation of the dispersal of maize (Zea mays ssp. mays) from south-central Mexico to the northern and southern limits of agriculture in the Western Hemisphere archaeologists and paleoethnobotanists are increasingly turning to the microbotanical record. Recent analysis of phytolith assemblages from charred cooking residues on pottery sherds in central New York recovered using 209 rondel phytolith variables has identified maize as early as 2270 ± 35 B.P. In this article we use discriminant analysis to re-classify these rondel phytolith assemblages resulting in only seven variables. The results are consistent with those achieved earlier using many more variables and a less formal statistical approach in terms of classification and in similarity of the original and reduced data matrix as seen by the Mantel test and cluster analyses.     

The Temple of Venus (Pompeii): a study of the pigments and painting techniques

We report here on a study of 57 fragments of wall painting excavated from the Temple of Venus (Pompeii). These samples were characterised by a wide range of analytical methods. Data showed that the palette is varied, although not so broad as that found in other buildings in Pompeii, and is consistent with pigments used elsewhere in Pompeii and in the Roman Empire. It is composed of: natural earths, minerals and rare artificial pigments. Paintings are made up of thin paint layers (0.01–0.10 mm thick) strongly adhering to the underlying preparation layer. Nonetheless, in some cases thicker layers (up to 0.40 mm) were recognised, often spread on other previous painting layers. Samples were also compared with the microstratigraphic criteria developed in Piovesan (2009) to distinguish wall painting techniques. This comparison demonstrated that both fresco and lime painting techniques were adopted.     

Identifying wine and oil production: analysis of residues from Roman and Late Antique plastered vats

The production of oil and wine was an important aspect of the ancient Mediterranean economy. Among the material remains related to the production of these substances, installations used for their production provide evidence that is still unexploited. Although archaeological studies have been carried out on these installations, problems can arise in the identification of their function, as wine and oil production structures can be similar and the archaeological traces insufficient to establish which substance was produced.