The challenge of identifying tuberculosis proteins in archaeological tissues

Hendy, Jessica; Collins, Matthew J.; Teoh, Kai Yik; Ashford, David A.; Thomas‐Oates, Jane; Donoghue, Helen D.; Pap, Ildikó; Minnikin, David E.; Spigelman, Mark; Buckley, Michael

doi:10.1016/j.jas.2016.01.003

Cited by 37 publications

(24 citation statements)

References 44 publications

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“…Like DNA, proteins undergo predictable forms of diagenetic alteration over time, so much so that there is an established field of amino acid / protein diagenesis geochronometry 98 , and documentation of diagenetic changes in ancient samples has been suggested as a useful authentication tool. In particular, diagenetically-induced modifications such as glutamine and asparagine deamidation and the presence of non-enzymatic cleavages of individual proteins are expected to occur in ancient samples 3,7,8,12,15,16 . Some studies have aimed to contrast such diagenetically-derived protein modifications between different proteins identified in the same sample 7,99 , allowing the potential separation of endogenous human proteins from contaminating human proteins.…”

Section: Data Interpretation and Authenticationmentioning

confidence: 99%

“…The advent of high-sensitivity mass spectrometry in the past two decades has allowed palaeoproteomics to become increasingly relevant in the fields of archaeology and evolutionary biology. Not only can individual proteins from archaeological and palaeontological contexts be studied, but one can also analyse the complex mixtures of proteins produced by individual organisms (proteomes) or groups of organisms (metaproteomes) found within ancient samples 1-3 . This has facilitated the phylogenetic reconstruction of extant and extinct species 2,[4][5][6] , including that of hominins 7 , the mechanistic investigation of protein degradation pathways 8 , studies of diagenetic and in vivo protein post-translational modifications (PTMs) [9][10][11] , the reconstruction of human diet and subsistence patterns 3,12 , and the characterization of past human diseases 3,[13][14][15][16] . The range of tissues and substrates that can be analyzed is similarly broad, including bone, antler, dentine and enamel 1,7,[17][18][19] , eggshell 8,20 , skin and soft tissues 13,14 , dental calculus 21 , preserved food remains [22][23][24][25] , potsherds and ceramic vessels [26][27][28] , bindings and glues [28][29][30][31] , paint binders [32][33]…”

Section: Introductionmentioning

confidence: 99%

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A guide to ancient protein studies

et al. 2018

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Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.

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Section: Data Interpretation and Authenticationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A guide to ancient protein studies

et al. 2018

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“…In addition to ancient DNA studies, the past few years have witnessed a multiplicity of analyses based on the extraction and characterisation of long-term persistent biomolecules: proteins [56][57][58][59][60][61] . Since their amino acid sequence is coded for by the DNA, proteins carry genetically derived features that allow researchers to propose phylogenetic relationships of extinct species [62][63][64][65] , sex attribution 66,67 or even characterisation of palaeopathogens 68 . The major protein of bone and teeth, type I collagen (constituting 90% of the organic phase of these materials), is composed of amino acid sequences that carry taxon-related differences in their order, allowing species discrimination 69 .…”

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confidence: 99%

Palaeoproteomics gives new insight into early southern African pastoralism

Meillour

Zirah

Zazzo

et al. 2020

Sci Rep

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The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the northeastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They are thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology, not only between these two domesticated caprine species, but also between them and the small wild antelopes, raised questions about the morphological species attribution of these remains. Additionally, the high fragmentation of the site's osteological remains makes it difficult to achieve species-level taxonomic identification by comparative anatomy. In this paper, we report molecular species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled with direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments. Understanding how past human populations interacted with their environment, and particularly with other animals, allows understanding large parts of societies, their organisation and their economy. Climatic change is one of the factors that may have pressured human populations to adapt their subsistence strategy and diet. With Saharan and Sahelian aridification starting at the end of the African Humid Period (ca. 14,800-5500 years before present [BP] 1), Africa experienced its last major climatic change 2 and humans had to adapt to new environments 3. Thus, the inception of domestication may have been constrained by fewer food resources and their increased unpredictability 4. Given that they have no wild representatives on the continent, it is now commonly accepted that domestic sheep (Ovis aries) and goat (Capra hircus) were introduced from the Near East 5,6. The first archaeozoological evidence of these species dates from the end of the 9th and the beginning of the 8th millennium BP, in the eastern part of the Sahara 7-13. Yet, their diffusion across the continent was slow: the first

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“…tuberculosis was not recovered in dental calculus (S6 Table). The lack of molecular evidence does not falsify the possibility of tubercular infection, but this case reiterates the difficulty of connecting epidemiological and bioarchaeological data [171].…”

Section: Discussionmentioning

confidence: 99%

"The dead shall be raised": Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut

et al. 2019

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In July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut’s first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven’s Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city’s rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery’s membership, and provide a template for future discoveries and analyses.

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The challenge of identifying tuberculosis proteins in archaeological tissues

Cited by 37 publications

References 44 publications

A guide to ancient protein studies

A guide to ancient protein studies

Palaeoproteomics gives new insight into early southern African pastoralism

"The dead shall be raised": Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut

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