Single-cell DNA analysis is not routinely carried out in a forensic setting as it is considered unreliable due to challenges associated with DNA amplification, contamination and profile interpretation. In light of the development of increasingly sensitive techniques, the question of the reliability of single-cell DNA analysis in terms of both processing and interpretation is addressed in the first part of this thesis. Optimising all stages of the DNA analysis process has provided a sensitive method which facilitates the successful outcome of a useable profile from single-cells. Although no consensus profile can be generated for this sample type, interpretation guidelines have been set to enable the robust analysis of single cells. It has been concluded that single-cells can be reliably amplified and profiled for forensic purposes. Both DNA and textile fibres have a proven track record in forensic casework yet their analysis is rarely combined. As an application of the aforementioned single-cell DNA analysis, this project explores the possibility that when fibres are transferred from one surface to another, they could also be acting as a vector for the wearer’s own DNA, through cells that have adhered to the fibre surfaces. Fluorescent staining and microscopy is used to detect the cells in situ on the fibre surface, which are then recovered and processed for DNA using the previously optimised single-cell analysis methods, along with a newly developed DNA assay designed for the amplification of low DNA template samples. The results of this study have demonstrated that cells can be visualised in situ on the fibre surface and that there is potential for cell transfer to occur. It has been concluded however, that from a casework point of view, targeting transferred fibres for cells may not be the best approach as it is time consuming and has not been shown to be effective in this study. The final part of this thesis is focused on the efficacy of massively parallel sequencing (MPS) technology for samples that are expected to be severely degraded due to age or exposure to a hostile environment. The ability of both the recently launched Illumina ForenSeq™ DNA Signature Prep Kit for nuclear DNA markers and an in-house method for the sequencing of degraded mitochondrial DNA, have been tested to determine if MPS offers a more comprehensive evaluation of degraded material than the traditional PCR-CE methods. The results of the ForenSeq kit have demonstrated the effectiveness of its low molecular weight STR and SNP markers for amplifying low template, degraded DNA samples, with alleles amplified using less than 20 pg total DNA input. This kit has also therefore shown application in the field of bioarchaeology, as it can provide the biological sex of the sample, biogeographic ancestry information and also aids detection of sample/control contamination. The in-house mitochondrial DNA assay resulted in the successful amplification and sequencing of samples for which no nuclear DNA was amplified. The high depth of read coverage in these samples, average of 18,000, allowed for the identification of even low level variants.

Yes

No description available.

Decorative, polychrome ceramics from Corinth, Greece, produced during the 8th-6th centuries B.C.E. are luxury goods that were widely traded throughout Greece and the Mediterranean. The decorated ceramics were produced in a variety of shapes, including aryballos, alabastron, and olpe. They were decorated with slip-glazes in distinctive white, black, red, yellow, and purple colors, and in a variety of surface finishes, matte, semi-matte and glossy. Artisans in Corinthian workshops experimented to change the colors of the slips by varying the type and amount of iron-rich raw materials. They also varied the composition of the clay used as a binder and the amount of flux used as a sintering aid to promote glass formation. This research reconstructs the technology used by the Corinthian craftsmen to produce the Archaic polychrome ceramics, and shows how these technologies differed from the production of better known, more prestigious Athenian black-figure and red-figure ceramics. Through microstructural examination of archaeological samples and replication experiments, this thesis proposes that the purple iron oxide pigment is the result of acid treatment and oxidation of iron metal. The firing temperature range of the Corinthian polychrome ceramics was determined experimentally to be 925-1025° C, which is higher than previously reported and similar to that reported for Corinthian transport amphoras. The firing range is higher by 50-150° C than the Athenian black-figure and red-figure ceramics. Samples of Corinthian polychrome and Athenian black-figure ceramics from the Marie Farnsworth collection at the University of Arizona were tested and compared to Corinthian clay collections. Analytical techniques included Fourier-transform infrared spectroscopy (FTIR), scanning-electron microscopy with energy-dispersive spectroscopy (SEM-EDS), micro-Raman spectroscopy, and wavelength-dispersive electron microprobe (EPMA with BSE-SEM).

In this paper, I discuss layer 23 from the 2015 excavation at the harbor in the black earth, Birka, through identification and conservation of a number of iron objects from this specific layer. These objects are in many cases broken and worn out, which indicates that they have been thrown away on purpose. Traces of bone and charcoal in the layer supports the idea that the harbor has been a place where people left their waste. Many of these excavated objects can be related to craftsmanship and/or the ships gear.

Archaeological bones are usually dated by radiocarbon measurement of extracted collagen. However, low collagen content, contamination from the burial environment or museum conservation work have previously lead to inaccurate results, especially for old bones, compromising the ability to reconstruct reliable past chronologies. It is reported, for example, that up to 70% of Palaeolithic radiocarbon dates on bones are likely to be underestimates of the real age, blurring the picture of modern human dispersals and Neanderthal extinction. In this thesis, a method for isolating and radiocarbon dating the collagen amino acid hydroxyproline is described. Hydroxyproline consists of about 10% of bone collagen but is not found in significant amounts elsewhere in nature. The hydroxyproline dating method uses a mixed-mode (i.e. ion-exchange combined with hydrophobic chemistry), semi preparative HPLC methodology. The amino acids do not require derivatisation, and no organic solvents are used, thereby avoiding addition of carbon. The hypothesis of this thesis is that the hydroxyproline can be used as a bone specific biomarker, improving dating accuracy and making it possible to obtain radiocarbon determinations where previously it has been impossible. It was calculated that on average 3.3±1.4μg of contaminant carbon are added to each sample in the process of isolating the hydroxyproline, a low level suitable for 14C dating. It was investigated whether a deliberately contaminated bone and 'naturally' contaminated archaeological bones, yielding erroneous dates when dated using the normal pretreatment method, could be dated accurately using this method. In addition, a hydroxyproline date was obtained for a bone with too little surviving collagen to be dateable by the bulk collagen method. Finally, using the hydroxyproline dating method, the earliest direct ages for the presence of anatomically modern humans on the Russian Plain were obtained. The method proved to be a powerful tool that can help resolve longstanding archaeological questions.

In an exploratory study, techniques were developed for isolating bulk plant proteins and measuring the ¹³C isotopic compositions of their constituent amino acids by HPLC-IRMS. Samples of plants expected to be of potential palaeodietary significance in northwestern Europe were selected for investigation. Different tissues of plants, leaves and seeds, may be distinguished from each other by the relative ¹³C isotopic compositions (‘isotopic signatures’) of the amino acids of their constituent proteins. For each tissue type, different plant types may be distinguished in the same way. These signatures can vary slightly according to environment and season, but the variation among types is greater than this. For leaves, isotopic signatures can be used to differentiate (i) nettles, (ii) true grasses, (iii) reeds etc, (iv) trees, (v) legumes, (vi) maize, (vii) freshwater plants and (viii) marine algae. For seeds, these signatures are able to differentiate (i) wheat-type cereals, (ii) barley-type cereals, (iii) C4 cereals, (iv) pseudocereals, (v) legumes and (vi) tree nuts. From investigations using a mixing model, it appears that these signals, particularly those of essential amino acids, are reflected in the tissues of their consumers. Freshwater plants are identified as the base of the food chain for dragonfly larvae, marine algae as the diet of marine molluscs and grass as the diet of archaeological cattle and aurochs. Isotopic ‘marine signals’ identified by previous researchers have been refined using these data and the isotopic signatures of fish muscle. These findings are expected to be of particular value in the study of palaeodiets using proteins from archaeological tissues, especially bone and hair. This approach will also find application in the fields of plant physiology and biochemistry.

Calcium isotope ratios (⁴⁴Ca/⁴²Ca) have shown promise as a milk dietary tracer. Previous studies have focused on bone but, due to homeostatic processes, δ^44/42Ca values are highly variable. This has greatly complicated the identification of mammal milk consumption through bone analysis, resulting in a search for an alternative. This thesis describes controlled studies to assess the effects of milk consumption on δ^44/42Ca values in bulk and sequential samples of dental enamel, using modern samples from Yorkshire, England, the Isle of Hoy, Scotland, and archaeological samples from Abu Hureyra, Syria. The samples from Yorkshire consisted of dental enamel, ewe milk, feed and bone. Dental enamel was sampled from the Hoy sheep. Milk and plants are the greatest contributors of calcium in the mammal diet. Feed and ewe milk samples confirmed that milk has lower δ^44/42Ca values than plants in the diet, and with a common diet between ewes, uniform milk δ^44/42Ca values are produced. Also, there is a significant difference between bulk molar enamel δ^44/42Ca values between males and females, with males having higher values. Additionally, analysis of bulk and sequential samples of Hoy mature sheep molar enamel, although mass fractionation effects were small, produced δ^44/42Ca values with a clear isotopic offset between the enamel likely formed during nursing, weaning and the full conversion to a plant diet. The δ^44/42Ca values, once associated with dental development chronologies, led to the identification of a clear pattern of nursing and weaning in the enamel of the first and second molars of sheep with known dietary and weaning histories. The modern results were used to identify patterns of ancient nursing and weaning. Although evidence was insufficient to establish early weaning of the Abu Hureyra sheep, this research successfully established the potential of this approach for investigating milk production and consumption in the archaeological record.

As a result of the quick rise of pXRF technology in archaeology, there are concerns regarding the reliability and validity of data output acquired from pXRF. In this study, I test the hypothesis that portable X-ray fluorescence (pXRF) spectrometry can provide reliable and valid results, using newly developed calibration curves, for the analysis of archaeological animal and human skeletal materials in prehistoric Peru to address hypotheses about ancient diet and trade. While pXRF systems may come with calibration software, the few if any standards and reference materials provided with the instrument rarely correspond to the vast array of archaeological materials capable of being analyzed by pXRF, including archaeological bone specimens. Empirical calibration curves for Ba, Ca, Fe, and Sr were created using the linear regression analysis of 19 human and animal bone standards analyzed via pXRF and ICP-MS. The results suggest the calibrations for Ca and Sr are sound, but the calibrations for Ba and Fe need to be further improved. In order to assess the reliability of pXRF (i.e. precision and accuracy), statistical analyses of 60 measurements on human bone specimens as well as on 19 human and animal bone specimens was performed in this study. The results indicate that the precision of pXRF is reliable, but additional work is needed with regard to accuracy. In contrast, the analysis of forty-four prehistoric human and animal bone specimens from varying regions in Peru were used to test the validity of pXRF. The pXRF data support the notion that pXRF is a valid technique to use in the analysis of bone specimens to address archaeological questions regarding paleodiet and possible trade interactions among individuals that reside in the highland and coastal valley regions of Peru

No description available.