Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies

Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Furthermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard extraction methods, without the need for specialised equipment or large-volume demineralisation steps.Denice Higgins, Adam B. Rohrlach, John Kaidonis, Grant Townsend, Jeremy J. Austi

Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures

Background: Teeth are a valuable source of DNA for identification of fragmented and degraded human remains. While the value of dental pulp as a source of DNA is well established, the quantity and presentation of DNA in the hard dental tissues has not been extensively studied. Without this knowledge common decontamination, sampling and DNA extraction techniques may be suboptimal. Targeted sampling of specific dental tissues could maximise DNA profiling success, while minimising the need for laborious sampling protocols and DNA extraction techniques, thus improving workflows and efficiencies. We aimed to determine the location of cellular DNA in non-degraded human teeth to quantify the yield of nuclear DNA from cementum, the most accessible and easily sampled dental tissue, and to investigate the effect of a common decontamination method, treatment with sodium hypochlorite (bleach). We examined teeth histologically and subsequently quantified the yield of nuclear DNA from the cementum of 66 human third molar teeth. We also explored the effects of bleach (at varying concentrations and exposure times) on nuclear DNA within teeth, using histological and quantitative PCR methods. Results: Histology confirmed the presence of nucleated cells within pulp and cementum, but not in dentine. Nuclear DNA yields from cementum varied substantially between individuals but all samples gave sufficient DNA (from as little as 20 mg of tissue) to produce full short tandem repeat (STR) profiles. Variation in yield between individuals was not influenced by chronological age or sex of the donor. Bleach treatment with solutions as dilute as 2.5% for as little as 1 min damaged the visible nuclear material and reduced DNA yields from cementum by an order of magnitude. Conclusions: Cementum is a valuable, and easily accessible, source of nuclear DNA from teeth, and may be a preferred source where large numbers of individuals need to be sampled quickly (for example, mass disaster victim identification) without the need for specialist equipment or from diseased and degraded teeth, where pulp is absent. Indiscriminant sampling and decontamination protocols applied to the outer surface of teeth can destroy this DNA, reducing the likelihood of successful STR typing results.Denice Higgins, John Kaidonis, Grant Townsend, Toby Hughes and Jeremy J. Austi

Synthetic and Mechanistic Investigation of an Oxime Ether Electrocyclization Approach to Heteroaromatic Boronic Acid Derivatives

E-oxime ethers are found to be significantly more reactive in electrocyclizations than their Z-counterparts because of an available transition state stabilizing orbital interaction in the former case. The scope of this chemistry to deliver useful heterocyclic products is also described

A 'Performative' Social Movement: The Emergence of Collective Contentions within Collaborative Governance

The enmeshment of urban movements in networks of collaborative governance has been characterised as a process of co-option in which previously disruptive contentions are absorbed by regimes and reproduced in ways that do not threaten the stability of power relations. Applying a theoretical framework drawn from feminist philosopher Judith Butler this paper directs attention to the development of collective oppositional identities that remain embedded in conventional political processes. In a case study of the English tenants' movement, it investigates the potential of regulatory discourses that draw on market theories of performative voice to offer the collectivising narratives and belief in change that can generate the emotional identification of a social movement. The paper originates the concept of the ‘performative social movement’ to denote the contentious claims that continue to emerge from urban movements that otherwise appear quiescent

Spatio-temporal patterns of fish assemblages in a large regulated alluvial river

1. The River Durance, the last alpine tributary of the River Rhone, is a large, braided alluvial hydrosystem. Following large-scale regulation, flow downstream of the Serre-Poncon dam has been maintained at 1⁄40th of previous annual mean discharge. To assess the effects of historical disturbances, fish assemblages and habitat use were analysed during five summers in a representative reach of the middle Durance. 2. Habitat availability and use were assessed with a multi-scale approach including the variables water depth, current velocity, roughness height of substratum, amount of woody debris and lateral⁄longitudinal location. Eighteen fish species were sampled by electrofishing in 289 habitat sample units. 3. Partial least square (PLS) regression showed that taxa were mainly distributed according to relationships between their total length and water depth⁄velocity variables. Fish assemblage composition was also related to roughness height as well as distance from the bank or to the nearest large woody debris. However, PLS regression revealed no significant differences in habitat selection between two periods of varying hydromorphological stability. 4. Fish distribution patterns and density were related to proximity to the bank and cover, indicating that local scale variables need to be considered in conservation and restoration programmes

Topography shapes the structure, composition and function of tropical forest landscapes.

Topography is a key driver of tropical forest structure and composition, as it constrains local nutrient and hydraulic conditions within which trees grow. Yet, we do not fully understand how changes in forest physiognomy driven by topography impact other emergent properties of forests, such as their aboveground carbon density (ACD). Working in Borneo - at a site where 70-m-tall forests in alluvial valleys rapidly transition to stunted heath forests on nutrient-depleted dip slopes - we combined field data with airborne laser scanning and hyperspectral imaging to characterise how topography shapes the vertical structure, wood density, diversity and ACD of nearly 15 km2 of old-growth forest. We found that subtle differences in elevation - which control soil chemistry and hydrology - profoundly influenced the structure, composition and diversity of the canopy. Capturing these processes was critical to explaining landscape-scale heterogeneity in ACD, highlighting how emerging remote sensing technologies can provide new insights into long-standing ecological questions

Factors associated with care-related Quality of Life of adults with Intellectual Disabilities in England: Implications for Policy and Practice

Over the last three decades, quality of life (QoL) has been advocated as an indicator of social care outcomes for adults with intellectual disabilities. In England, the Adult Social Care Survey (ASCS) is conducted annually by local authorities to contribute to the evidence base of the care-related QoL of people receiving publicly-funded adult social care. This study explores relationships between QoL and non-care related factors to identify relationships that could inform social care policy and practice. Cross-sectional data collected from 13,642 adults who participated in the 2011 and 2012 ASCS were analysed using regression to explore the factors associated with QoL measured using the Adult Social Care Outcomes Toolkit (ASCOT). Self-rated health, rating of the suitability of home design and anxiety/depression were all found to be significantly associated with ASCOT. Other individual and survey completion factors were also found to have weak significant relationships with ASCOT. The models also indicate that there was an increase in overall ASCOT-QoL and in five of the eight ASCOT domains (Personal comfort and cleanliness, Safety, Social participation, Occupation and Dignity) between 2011 and 2012. These findings demonstrate the potential value of QoL data for informing policy for people with intellectual disabilities by identifying key factors associated with QoL, the characteristics of those at risk of lower QoL, and QoL domains that could be targeted for improvement over time. Future research should establish causal relationships and explore the risk-adjustment of scores to account for variation outside of the control of social care support