Noreen Tuross

Asprich: A novel aspartic acid-rich protein family from the prismatic shell matrix of the bivalve Atrina rigida.

Almost all mineralized tissues contain proteins that are unusually acidic. As they are also often intimately associated with the mineral phase, they are thought to fulfill important functions in controlling mineral formation. Relatively little is known about these important proteins, because their acidic nature causes technical difficulties during purification and characterization procedures. Much effort has been made to overcome these problems, particularly in the study of mollusk‐shell formation. To date about 16 proteins from mollusk‐shell organic matrices have been sequenced, but only two are unusually rich in aspartic and glutamic acids. Here we screened a cDNA library made from the mRNA of the shell‐forming cells of a bivalve, Atrina rigida, using probes for short Asp‐containing repeat sequences, and identified ten different proteins. Using more specific probes designed from one subgroup of conserved sequences, we obtained the full sequences of a family of seven aspartic acid‐rich proteins, which we named “Asprich”; a subfamily of the unusually acidic shell‐matrix proteins. Polyclonal antibodies raised against a synthetic peptide of the conserved acidic1 domain of these proteins reacted specifically with the matrix components of the calcitic prismatic layer, but not with those of the aragonitic nacreous layer. Thus the Asprich proteins are constituents of the prismatic layer shell matrix. We can identify different domains within these sequences, including a signal peptide characteristic of proteins destined for extracellular secretion, a conserved domain rich in aspartic acid that contains a sequence very similar to the calcium‐binding domain of Calsequestrin, and another domain rich in aspartic acid, that varies between the seven sequences. We also identified a domain with DEAD repeats that may have Mg‐binding capabilities. Although we do not know, as yet, the function of these proteins, their generally conserved sequences do indicate that they might well fulfill basic functions in shell formation.

Ancient DNA analysis of human populations

The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA.

Strontium increases and crystallinity changes in taphonomic and archaeological bone

Bone strontium levels and hydroxyapatite crystal sizes increased with time in two exposed wildebeest skeletons. The strontium increases could not be removed by sequential washing according to the method of Sillen, A. (1986). Biogenic and diagenetic SrCa in Plio-Pleistocene fossils of the Omo Shungura Formation. Paleobiology12, 311–323. Human subfossil bone recovered archaeologically also showed evidence of extensive diagenetic reworking that resulted in crystal growth and elevated strontium levels. The increase in bone strontium content was independent of nonapatitic contaminating crystal phases.

Transformation of plant biochemicals to geological macromolecules during early diagenesis

Abstract Chemical and isotopic changes in plant biochemicals that were transformed into organic geochemicals have been measured in anaerobic, freshwater marsh environments. In two litter bag studies, plant biochemicals decayed extensively in the first year, as recorded by dry weight, C:N ratios, δ15N of bulk tissue and amino acids, and δ13C of individual amino acids. Molecular analyses of Rubisco revealed that the high-molecular-weight enzyme subunit could be recognized antigenically for at least 12 months, but concentrations and amounts declined. Geochemical compounds, advanced glycation endproducts, were not found in fresh plants, but formed gradually with first indications documented at 3 months. The organic remains of plants were reworked or replaced by microbial products from decomposition, as indicated by a shift in the isotopic composition of individual amino acids in total plant protein. In experiments with Rubisco, isotopic changes over time in the individual amino acids in the 50–60 kDa molecular weight range were substantial. These high-molecular-weight substances were no longer pristine molecules. Biochemical and isotopic tools for studying living processes have been demonstrated to be effective and novel approaches to identify and quantify altered geochemical remnants.

Extending the limits of paleodietary studies of humans with compound specific carbon isotope analysis of amino acids

Stable carbon isotopes in the bone collagen of prehistoric humans are valuable tools for determining human diet. We studied carbon isotopes in individual amino acids (IAA) in plants and collagen from herbivores and humans from North American prehistoric sites in order to determine whether more specific dietary information about Indians could be predicted. The 13 C of plant amino acids ranged extensively, whereas 13 C values of each amino acid from the C3 (n3) and C4 (n3) plant species were linearly related with a slope of 0.8. Essential amino acids from herbivores had 13 C values that were completely different from those measured in either C3 or C4 plants, suggesting metabolic resynthesis in the gut by microflora. The 13 C of essential amino acids from prehistoric North Americans, who had diets ranging from primarily maize-based (C4) to hunter-gathers (C3) subsistence, were highly correlated with 13 C values of herbivore essential amino acids. There was no significant correlation of 13 C in IAA from humans with those of plants. The 13 C of nonessential amino acids in human bone collagen can distinguish the presence of maize in the diet, whereas the 13 C of essential amino acids were transparent to a maize-derived carbon signal. Compound specific isotopic data on IAA distinguish between total carbon intake versus total protein intake and are useful for discerning the extent and nature of omnivory.

Identification of Treponema pallidum Subspecies pallidum in a 200-Year-Old Skeletal Specimen

Treponema pallidum subsp. pallidum, the causative agent of venereal syphilis, was detected in a 200-year-old skeletal specimen from Easter Island. An initial diagnosis of treponemal infection was confirmed by extensive purification of immunoglobulin that reacted strongly with T. pallidum antigen. Extracted DNA exhibited a single-base polymorphism that distinguished T.p. subsp. pallidum from 4 other human and nonhuman treponemes. Extensive precautions against contamination of the subject matter with modern treponemal DNA were employed, including analysis of archaeological and modern specimens in 2 geographically separate laboratories. Molecular determination of historical disease states by using skeletal material can significantly enhance our understanding of the pathology and spread of infectious diseases.

Monitoring the routing of dietary and biosynthesised lipids through compound--specific stable isotope (delta 13C) measurements at natural abundance.

mother’s cousins’ grand-offspring of the workers [13, 14]. This hardly suggests that the wasps will be unwilling to rear brood of different levels of relatedness. The most likely explanation for our results is therefore that cofoundresses forced to nest alone are incapable of rearing as much brood as queens forced to nest alone or a solitary foundress, and hence we suggestion that wasps may choose their nesting strategies based on their broodrearing abilities.

Organic oxygen and hydrogen isotopes in a porcine controlled dietary study

Controlled feeding studies have been useful in assessing the relationship between isotope values from dietary sources and consumer tissues. We report the organic oxygen and hydrogen values of animal tissue from a porcine controlled dietary study. A complex mixture of fractionation and incorporation is revealed. In both deltaD and delta(18)O, differences in the absolute values and the amount of variation between and within consumer tissue are documented. Significant differences in deltaD and delta(18)O are observed between protein sources such as keratin and collagen.

Brief communication: Tissue isotopic enrichment associated with growth depression in a pig: Implications for archaeology and ecology

Stressors such as fasting or poor diet quality are thought to potentially alter the nitrogen and carbon isotopic values of animal tissues. In this study, we demonstrate an inverse correlation between growth rate and multiple tissue enrichment of delta(15)N, delta(13)C, and, to a lesser degree, delta(18)O in a juvenile pig. A more complex pattern is observed with respect to tissue deltaD and growth rate. The observed association between growth rate and tissue isotopic fractionation has important implications for paleodietary and migratory reconstructions of archaeological populations that may have been affected by famine, malnutrition, seasonal variation in food availability, and/or other factors that can affect childhood growth rates.

Finding Fodder and Tracking Transhumance: Isotopic Detection of Goat Domestication Processes in the Near East

The domestication of several animal taxa in the Near East approximately 10,000 years ago marked a fundamental shift in human-animal interactions that irrevocably transformed the subsistence base of prehistoric societies. Domesticates eventually provided humans with an easily accessible source of animal products including meat, milk, and hair, but the mechanisms by which humans first experimented with and domesticated their animals remain poorly understood. Early animal management strategies included the selective harvesting of juvenile males while promoting female survivorship, but other husbandry practices that contributed to the domestication of animals have proven elusive in the archaeological record. Here we apply a novel multistable isotopic approach (δ13C, δ15N, and δ18O) to bone collagens recovered from goats—one of the first animal domesticates—and wild gazelles from two Early Neolithic sites in the Near East. We show that humans provisioned goats with fodder and mobilized herds to different pastures as early as 8000 cal BC. By enacting these particular husbandry practices, prehistoric humans effectively increased the accessibility and predictability of their own food supply and ultimately came to domesticate multiple animal taxa.