Biomolecular archaeology
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Recent papers in Biomolecular archaeology
Sedimentary ancient DNA (sedaDNA) has been established as a viable biomolecular proxy for tracking taxon presence through time in a local environment, even in the total absence of surviving tissues. SedaDNA is thought to survive through... more
Sedimentary ancient DNA (sedaDNA) has been established as a viable biomolecular proxy for tracking taxon presence through time in a local environment, even in the total absence of surviving tissues. SedaDNA is thought to survive through mineral binding, facilitating long-term biomolecular preservation, but also challenging DNA isolation. Two common limitations in sedaDNA extraction are the carryover of other substances that inhibit enzymatic reactions, and the loss of authentic sedaDNA when attempting to reduce inhibitor co-elution. Here, we present a sedaDNA extraction procedure paired with targeted enrichment intended to maximize DNA recovery. Our procedure exhibits a 7.7-19.3x increase in on-target plant and animal sedaDNA compared to a commercial soil extraction kit, and a 1.2-59.9x increase compared to a metabarcoding approach. To illustrate the effectiveness of our cold spin extraction and PalaeoChip capture enrichment approach, we present results for the diachronic presence of plants and animals from Yukon permafrost samples dating to the Pleistocene-Holocene transition, and discuss new potential evidence for the late survival (~9700 years ago) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike region of Yukon, Canada. This enrichment approach translates to a more taxonomically diverse dataset and improved on-target sequencing.
Extracción de ADN mitocondrial de una momia infantil fechada hacia el 300 a.C. encontrada en un abrigo rocoso de la Sierra Gorda, Querétaro, México.
Sex estimation of skeletons is fundamental to many archaeological studies. currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods... more
Sex estimation of skeletons is fundamental to many archaeological studies. currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation. Biological sex plays an important role in the human experience, correlating to lifespan, reproduction, and a wide range of other biological factors 1-5. Sex and gender are also fundamental in structuring an array of cultural behaviors, including residence patterns, kinship, economic roles, and identity construction and expression 6-9. How sex interacts with gender and these particular issues is not static and can vary in detail across societies and over time 10-12. It is not surprising that sex is one of the most basic and important measures in bioarchaeological and forensic analyses. Typically, osteological features are used to estimate sex of skeletal remains, and the most widely used marker is the morphology of the os coxae 13-16. However, appropriate markers are not always sufficiently expressed or preserved to estimate sex using morphological criteria 17. A lack of sexually-dimorphic markers is especially acute for skeletons of infants and children who have not undergone puberty. Mortuary practices, such as cremation or secondary burial in charnel houses, can also can impose limitations on the utility of osteological sex estimates 18. The advent of DNA sequencing made it possible to use skeletal remains to estimate the sex of very young individuals ; it also expanded sex estimations for fragmentary, pathological, and degraded skeletal materials 19-21. More recently, development of massively parallel DNA sequencing greatly improved genome coverage in archaeological samples 22-25. In addition to providing detailed genetic information, this allows biological sex to be estimated from shotgun sequencing data 25-27. These approaches were an improvement over earlier PCR-based marker open
For a long time, the nutritional practices of Ancient Egypt were discussed on the basis of written, pictorial and archaeobotanical sources. Especially the hieratically inscribed vessels of the New Kingdom seemed to be a reliable source... more
For a long time, the nutritional practices of Ancient Egypt were discussed on the basis of written, pictorial and archaeobotanical sources. Especially the hieratically inscribed vessels of the New Kingdom seemed to be a reliable source for the stored and consumed food. At the same time, it has not yet been possible to understand all the terms for foodstuffs. The poster presents the results of our first series of organic residue analyses (ORA) from labelled vessels from Amarna, today in the British Museum. Correlations between inscription and content, but also complex usage biographies and information on trading mechanisms are discussed.
Chemical analysis of archaeological artefacts is used with increasing regularity to understand how wine was produced, traded, and consumed in the past and to shed light on its antiquity. Based both on an extensive review of the published... more
Chemical analysis of archaeological artefacts is used with increasing regularity to understand how wine was produced, traded, and consumed in the past and to shed light on its antiquity. Based both on an extensive review of the published literature and on new analyses, here we critically evaluate the diverse range of methodological approaches that have been used for wine identification. Overall, we conclude that currently none of the proposed chemical 'biomarkers' for wine provide unequivocal evidence. Nevertheless, valid interpretations may be offered if systematically supported by additional contextual data, such as archaeobotanical evidence. We found the extraction and detection method to be particularly crucial for successful identification. We urge the use of controls and quantification to rule out false positives. DNA sequencing offers potential for identifying wine and provides much higher taxonomic resolution, but work is needed to determine the limits of DNA survival on artefacts.
Drinking had been very important in the Classical period societies. Drinking appeared to be a social convention practice at weddings, funerals, religious activities, diplomacy affairs and establishing long-lasting relationships. Countless... more
Drinking had been very important in the Classical period societies. Drinking appeared to be a social convention practice at weddings, funerals, religious activities, diplomacy affairs and establishing long-lasting relationships. Countless evidence for drinking practices during religious festivals, political domestic and foreign meetings comes from the Ancient Greek written sources. While the sources present detailed narratives about these practices among the Greeks, very little is said about drinking in foreign societies. For that reason, the most valuable materials to reconstruct important social behavior in the known- Greek lands appeared to be the material remains from the Archaeological sites.
In the last few decades, hundreds of objects related to drinking practices were found in the burial sites in South Bulgaria, the Bulgarian part of Thrace. The evidence pointed out that this territory was extensively inhabited from a very early period. In the Classical period, V-th – IV-the centuries BC the territory was a homeland of the Thracian tribes who established at the beginning of the V-th century the first stable state organization, the Odrysian Kingdom.
In the last few decades, hundreds of objects related to drinking practices were found in the burial sites in South Bulgaria, the Bulgarian part of Thrace. The evidence pointed out that this territory was extensively inhabited from a very early period. In the Classical period, V-th – IV-the centuries BC the territory was a homeland of the Thracian tribes who established at the beginning of the V-th century the first stable state organization, the Odrysian Kingdom.
The extraction and study of organic residues from ceramics has been a subject of interest for the last 50 years in archeology and archeological science. Lipids are among the best-preserved organic substances in archeological contexts and... more
The extraction and study of organic residues from ceramics has been a subject of interest for the last 50 years in archeology and archeological science. Lipids are among the best-preserved organic substances in archeological contexts and can provide information about the diets of ancient populations as well as past environments. Here, we present a method which demonstrates significantly improved extraction of lipids from archeological pots by replacing liquid organic solvents with supercritical fluids. Optimization of the procedure using response surface methodology (RSM) approach showed that, on our system, optimal conditions for supercritical extraction of lipids from synthetic fired clay ceramics could be achieved using carbon dioxide with 16 vol % of cosolvent EtOH−H 2 O (95:5 v/ v) in 90 min at a flow rate of 2.3 mL/min, for a pressure of 30 MPa and a temperature of 50 °C. For all reference and archeological samples included in this study, lipid yields obtained by supercritical fluid extraction under these optimal conditions were systematically higher than by conventional solvent extraction. This study also highlighted a variability of the ratio of unsaturated versus saturated fatty acids depending on the extraction method. This can have important implications in the identification of the residue(s). The increased extraction efficiency provided by supercritical fluids, as well as their minimally destructive nature, enable new and refined approaches to residue analysis and dating of archeological ceramics. A rchaeological investigations of lives and lifestyles of human populations in the past are based, almost exclusively, on studies of material remains such as stone tools, ceramic vessels, glass or metal artifacts, textiles, and other organic substances (i.e., bone, wood, charcoal, seeds). Archaeologists have always relied on scientific methods to enrich their interpretations of these remains, and over the last few decades, techniques to characterize organic substances at a molecular level have improved dramatically. This trend is seen clearly in the ever-expanding application of analytical techniques based on the use of chromatography and mass spectrometry (e.g., high-performance liquid chromatography (HPLC) and gas chromatography/ mass spectrometry (GC/MS)). 1 Although these techniques have many applications in archeological science, the most common relates to the question of ancient diet and the analysis of ancient food residues preserved within the fabric of ceramic containers. 2−4 To exploit this valuable source of information, scientists conventionally pulverize fragments of pottery and apply a combination of liquid organic solvents such as chloroform or dichloromethane and methanol. Other approaches using chemical reagents (e.g. acidified methanol) have also been explored. 5 The extracted residue is then characterized by GC/MS or GC-C-IRMS. 4 This is a time-consuming process which requires toxic solvents and is also destructive as the sherd needs to be crushed to increase the surface interface between ceramic and solvent. Over the last few decades, the field of analytical chemistry has seen substantial transformations such as with the development and application of new instrumentation using supercritical fluids (SFs) for extraction and chromatographic separation (SFE and SFC, respectively). In the field of archeological science, the use of supercritical fluids has not yet been fully
Lange Zeit wurden die Ernährungspraktiken des Alten Ägypten wesentlich anhand von schriftlichen, bildlichen und archäobotanischen Quellen diskutiert. Insbesondere die hieratisch beschrifteten Gefäße des Neuen Reichs schienen eine... more
Lange Zeit wurden die Ernährungspraktiken des Alten Ägypten wesentlich anhand von schriftlichen, bildlichen und archäobotanischen Quellen diskutiert. Insbesondere die hieratisch beschrifteten Gefäße des Neuen Reichs schienen eine zuverlässige Quelle für die gelagerten und konsumierten Lebensmittel. Zugleich war es aber bislang nicht möglich, alle der hieratischen Inhaltsangaben auch zu verstehen. Ziel unseres Projekts „FoodTransforms. Transformations of Food in the Eastern Mediterranean Late Bronze Age“ ist es unter anderem, mittels chemischer Nahrungsrückstandsanalysen den Zusammenhang zwischen den Inhaltsangaben auf dem Gefäß und den anhand von Rückständen zu identifizierenden Inhalten zu entschlüsseln. Im Rahmen dieses Vortrags möchten wir die Ergebnisse unserer ersten Analyseserien vorstellen, die sich auf die hieratisch beschrifteten Gefäße aus dem Ramesseum und aus Amarna konzentrierte. Unsere Analysen zeigen nicht nur die auch erwarteten Korrelationen zwischen Beschriftung und Inhalt, sondern zudem komplexe Nutzungsbiographien der Objekte und damit verbundene Widersprüche zwischen Beschriftungen und tatsächlichen Inhalten. Dem methodologischen Paradigma der diesjährigen SÄK entsprechend, möchten wir das Potential und die Grenzen naturwissenschaftlicher Nahrungsrückstandsanalysen für das Verständnis von Ernährungs-, Vorrats- und Beschriftungspraktiken im Neuen Reich diskutieren.
Il testo che segue riguarda la nostra ricerca archeologica sulla Sicilia bizantina, islamica e normanno-sveva e in particolare riporta le ultime scoperte a Castronovo di Sicilia, che includono il riconoscimento di una chiesa del XII-XIII... more
Il testo che segue riguarda la nostra ricerca archeologica sulla Sicilia bizantina, islamica e normanno-sveva e in particolare riporta le ultime scoperte a Castronovo di Sicilia, che includono il riconoscimento di una chiesa del XII-XIII secolo sul Monte Kassar, la continuazione dello scavo a Casale San Pietro e una sintesi delle nuove ricognizioni nelle sue vicinanze. Quest’ultimo sito rimane il focus principale del Progetto ERC sictransit, ma in questa sede diamo anche conto dei primi risultati di un’indagine più ampia, che include una grossa quantità di reperti che provengono da tutta la Sicilia da siti scavati in precedenza (Fig 1). Questi reperti consistino in ceramiche, metalli e vetri assieme a resti umani, animali e vegetali, che vengono analizzati nei laboratori delle università partner del progetto: York, Roma e Lecce. I principali metodi scientifici applicati sono: analisi tipologiche, petrografiche e del contenuto organico delle ceramiche da cucina e da tra-sporto; degli isotopi stabili e del DNA antico sui resti umani e animali per determinare la dieta e l’ascendenza genetica; infine la identificazione tassonomica e la caratterizzazione isotopica degli insiemi di resti botanici per comprendere le loro relazioni con il clima e con le diverse fasi storiche. Il progetto “Sicily in Transition” (acronym: Sictransit) combina quindi ricerche archeologiche, bioarcheologiche e biomolecolari in un unico progetto integrato. Gli obiettivi attesi sono stati suddivisi, per comodità e chiarezza, in tre principali aree di studio, vale a dire: agricoltura (e cibo), scambi e demografia. Infine concludiamo con una valutazione della ricerca svolta sul campo e delle prospettive di indagine dei tre laboratori
We are offering two lectureships in archaeology, one in Cultural Heritage and one in Ancient Biomolecules. Applications closing May 12. Please have a look and circulate.
Molecular and isotopic analysis of sediments from archaeological combustion features is a relatively new area of study. Applications can inform us about ancient pyro-technologies and patterns of animal exploitation in a wide range of... more
Molecular and isotopic analysis of sediments from archaeological combustion features is a relatively new area of study. Applications can inform us about ancient pyro-technologies and patterns of animal exploitation in a wide range of human contexts, but may be particularly informative with regard to ancient hunter-gatherers. Our analyses of sediments from experimental bone and wood fires, and from controlled laboratory heating sequences, provide fine-grained data on the formation and location of biomarkers from pyrolyzed animal fats in hearths. Integrating microstratigraphic, molecular and isotopic data can improve recognition of bone fires in archaeological contexts, perhaps even where bone preservation is poor. Experimental bone fires produced an upper layer of calcined bone above a thin layer of tarry-black amorphous material coating mineral sediments. Mineral sediments beneath the black layer showed little alteration but high lipid content. Sampling for molecular and isotopic analysis should target the black layer as the bulk of pyrolyzed biomarkers are located here and stable isotope values are less affected than in the overlying layer of ash or calcined bone. The combined presence of certain symmetric and slightly asymmetric saturated long-chain ketones (14-nonacosanone, 16-hentriacontanone, 16-tritriacontanone, and 18-pentatriacontanone), especially together with heptadecane (C17 n-alkane), are molecular indicators of the thermal degradation of terrestrial animal fat. Formation and relative dominance of these molecules in hearth sediments relates to the initial prevalence of specific precursor fatty acids and can provide broad separations between sources. We suggest that separations could be further supported and expanded by combining stable isotope analysis of the same compounds.
The spread of early farming across Europe from its origins in Southwest Asia was a culturally transformative process which took place over millennia. Within regions, the pace of the transition was probably related to the particular... more
The spread of early farming across Europe from its origins in Southwest Asia was a culturally transformative process which took place over millennia. Within regions, the pace of the transition was probably related to the particular climatic and environmental conditions encountered, as well as the nature of localized hunter–gatherer and farmer interactions. The establishment of farming in the interior of the Balkans represents the first movement of Southwest Asian livestock beyond their natural climatic range, and widespread evidence now exists for early pottery being used extensively for dairying. However, pottery lipid residues from sites in the Iron Gates region of the Danube in the northern Balkans show that here, Neolithic pottery was being used predominantly for processing aquatic resources. This stands out not only within the surrounding region but also contrasts markedly with Neolithic pottery use across wider Europe. These findings provide evidence for the strategic diversity within the wider cultural and economic practices during the Neolithic, with this exceptional environmental and cultural setting offering alternative opportunities despite the dominance of farming in the wider region.
The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled... more
The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan’s high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies.
Zooarchaeology can be most broadly defined as the systematic study of animal remains from archaeological contexts. One of the primary aims of zooarchaeological research has been to address questions pertaining to the utilization of animal... more
Zooarchaeology can be most broadly defined as the systematic study of animal remains from archaeological contexts. One of the primary aims of zooarchaeological research has been to address questions pertaining to the utilization of animal resources by humans, with a particular emphasis on dietary and environmental reconstructions. In most cases, the presence of faunal remains at an archaeological site is assumed to represent the use of locally obtained resources. In recent decades, increasing attention has been devoted to the investigation of faunal evidence pertaining to patterns of human migration and trade. In fact, faunal remains often provide some of the clearest evidence for past human migrations and for long‐distance interactions between groups, such as trade and exchange. Examples of zooarchaeological insights on these topics span a vast range of materials (calculus, coprolites, feathers, hair, horns, shells, teeth, wool, leather and parchment, bones, ivory), scales (local, regional, continental), and behavior (hunting, herding, husbandry, trade, exchange, translocations).
As organic materials, fish and its derivative products are perishable and break down rapidly and ultimately disappear. Unless they include bones or scales, the only means of identifying them in the archaeological record is through the... more
As organic materials, fish and its derivative products are perishable and break down rapidly
and ultimately disappear. Unless they include bones or scales, the only means of identifying
them in the archaeological record is through the identification of the chemical constituents
that are left behind after decomposition. Fish flesh mainly consists of proteins
and lipids. Since these molecules are unstable they degrade irreversibly after death or discard,
losing a significant part of the original chemical elements, consequently hampering
or complicating their identification. In this paper, two main types of fish products are considered:
raw, salted or cooked fish, and fermented fish-based products. In the first case,
the degradation of the native markers results from chemical post-depositional degradation,
and eventually thermal degradation during cooking. In the second case, the biochemical
processes involve bacteria that cause the rapid decomposition of fish as part of the process
of forming fish sauces, such as Roman garum. To detect and identify fish products we combined
experimental archaeology and organic analyses. The identification of the degradation
products of cholesterol appeared to provide a strong indicator for detecting the presence
of fish sauces. Analysis of samples taken from fish-salting vats located along the Atlantic
coast (Marsa, Baelo Claudia, Troia, Kerlaz, and Etel) with samples taken from actual
experimental garum sauces made from mackerel (Scomber scombrus), sardines (Sardina
pilchardus), and/or oysters (Ostreidae), revealed the presence of common markers of fermented
fish-based products. The application of the analytical methodology described here
to structures involved in ancient fish sauce manufacture and storage has enabled investigation
of the production of the sauces by searching directly for the fish markers on the inner
sides of the containers. For the first time the addition of molluscs and fruits in the fish
product has been identified as part of the process of manufacturing garum.
and ultimately disappear. Unless they include bones or scales, the only means of identifying
them in the archaeological record is through the identification of the chemical constituents
that are left behind after decomposition. Fish flesh mainly consists of proteins
and lipids. Since these molecules are unstable they degrade irreversibly after death or discard,
losing a significant part of the original chemical elements, consequently hampering
or complicating their identification. In this paper, two main types of fish products are considered:
raw, salted or cooked fish, and fermented fish-based products. In the first case,
the degradation of the native markers results from chemical post-depositional degradation,
and eventually thermal degradation during cooking. In the second case, the biochemical
processes involve bacteria that cause the rapid decomposition of fish as part of the process
of forming fish sauces, such as Roman garum. To detect and identify fish products we combined
experimental archaeology and organic analyses. The identification of the degradation
products of cholesterol appeared to provide a strong indicator for detecting the presence
of fish sauces. Analysis of samples taken from fish-salting vats located along the Atlantic
coast (Marsa, Baelo Claudia, Troia, Kerlaz, and Etel) with samples taken from actual
experimental garum sauces made from mackerel (Scomber scombrus), sardines (Sardina
pilchardus), and/or oysters (Ostreidae), revealed the presence of common markers of fermented
fish-based products. The application of the analytical methodology described here
to structures involved in ancient fish sauce manufacture and storage has enabled investigation
of the production of the sauces by searching directly for the fish markers on the inner
sides of the containers. For the first time the addition of molluscs and fruits in the fish
product has been identified as part of the process of manufacturing garum.
The European high Alps are internationally renowned for their dairy produce, which are of huge cultural and economic significance to the region. Although the recent history of alpine dairying has been well studied, virtually nothing is... more
The European high Alps are internationally renowned for their dairy produce, which are of huge cultural and economic significance to the region. Although the recent history of alpine dairying has been well studied, virtually nothing is known regarding the origins of this practice. This is due to poor preservation of high altitude archaeological sites and the ephemeral nature of transhumance economic practices. Archaeologists have suggested that stone structures that appear around 3,000 years ago are associated with more intense seasonal occupation of the high Alps and perhaps the establishment of new economic strategies. Here, we report on organic residue analysis of small fragments of pottery sherds that are occasionally preserved both at these sites and earlier prehistoric rock-shelters. Based mainly on isotopic criteria, dairy lipids could only be identified on ceramics from the stone structures, which date to the Iron Age (ca. 3,000-2,500 BP), providing the earliest evidence of this practice in the high Alps. Dairy production in such a marginal environment implies a high degree of risk even by today's standards. We postulate that this practice was driven by population increase and climate deterioration that put pressure on lowland agropastoral systems and the establishment of more extensive trade networks, leading to greater demand for highly nutritious and transportable dairy products.
The Early Copper Age in the Southeastern Alpine region and in the Western Pannonia is characterized by particular material culture, in Western Hungary called Balaton-Lasinja Culture, in Southern Austria Kanzianiberg-Lasinja, and in... more
The Early Copper Age in the Southeastern Alpine region and in the Western Pannonia is characterized by particular material culture, in Western Hungary called Balaton-Lasinja Culture, in Southern Austria Kanzianiberg-Lasinja, and in Northern Croatia and Continental Slovenia simply Lasinja Culture. Archaeological research showed that pottery of this culture presents connections with the late Vinča Culture, which attests the earliest copper mining and copper smelting activities in Europe, and especially to the subsequent Salcuta-Krivodol Culture of the Central Balkan. One particular find that shows connections to the Vinča Culture are miniature bottles. Although they are not common, their findspots are distributed almost entirely in the Southeastern Alpine region. Their particular shape suggests that they were used for storing small quantities of goods, while their small, perforated handles indicate that they were hung with rope around the neck or behind the waist of selected members of society. This paper discusses the use and the importance of this particular find dating to the Eneolithic period in the Southeastern Alpine region based on the multi-analytical approach. The possible function of miniature bottles was studied one hand through analysis of the finding locations, typological analysis and ethnographic parallels, and on the other hand by a state of the art archaeometric analytics like nondestructive micro X-ray diffraction of the still existing content of one bottle and biomolecular techniques.
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