Michael S. Riley

The thermal history of human fossils and the likelihood of successful DNA amplification

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.

Neanderthal DNA: Not just old but old and cold?

The successful retrieval of ancient DNA from two geographically dispersed Neanderthal skeletons has fuelled a demand for more Neanderthal DNA sequences for analysis. However, these exceptionally well-preserved specimens were geologically young and the mean annual temperature of their cave sites low, so the survival of this ancient DNA could have been due to unusually favourable conditions. Here we calculate the thermal history of a range of Holocene and Pleistocene bones whose DNA quality has been tested and find that in only very few sites with Neanderthal remains is the preservation of DNA likely to match the quality of that from the skeleton found at Mezmaiskaya Cave. We recommend that any additional Neanderthal destined for destructive analysis should be carefully selected, taking into account its integrated thermal history.

A field and modeling study of fractured rock permeability reduction using microbially induced calcite precipitation.

Microbially induced calcite precipitation (MICP) offers an attractive alternative to traditional grouting technologies for creating barriers to groundwater flow and containing subsurface contamination, but has only thus far been successfully demonstrated at the laboratory scale and predominantly in porous media. We present results of the first field experiments applying MICP to reduce fractured rock permeability in the subsurface. Initially, the ureolytic bacterium, Sporosarcina pasteurii, was fixed in the fractured rock. Subsequent injection of cementing fluid comprising calcium chloride and urea resulted in precipitation of large quantities (approximately 750 g) of calcite; significant reduction in the transmissivity of a single fracture over an area of several m(2) was achieved in around 17 h of treatment. A novel numerical model is also presented which simulates the field data well by coupling flow and bacterial and solute reactive transport processes including feedback due to aperture reduction via calcite precipitation. The results show that MICP can be successfully manipulated under field conditions to reduce the permeability of fractured rock and suggest that an MICP-based technique, informed by numerical models, may form the basis of viable solutions to aid pollution mitigation.

An Algorithm for Generating Rock Fracture Patterns: Mathematical Analysis

A statistical, rule-based algorithm for generating fracture patterns similar to those observed in Limestone is presented. For each fracture set, initial seed points are randomly positioned within the modelled domain with the same density as the fractures observed in the field. An orientation is associated with each point by sampling from the distribution of orientations for the corresponding fracture set. Fractures are then allowed to grow from the seed points in both directions with this orientation until they meet other fractures whereupon they continue or terminate according to a fixed probability. A mathematical analysis of this method is presented for the case in which fractures within a set are assumed to be parallel. Approximations to the distribution of semi-trace lengths are derived which are shown to be in good agreement with simulation results. Fracture spacing distributions are also derived for this case.

Long-term trends in the survival of immunological epitopes entombed in fossil brachiopod skeletons

Abstract We report the most comprehensive study of survival of peptide bonds and epitopes (antibody binding sites) in fossil shells from a semi-continuous New Zealand brachiopod sequence extending for 3 Ma. The study reveals for the first time long-term trends in proteins survival. The investigation focused on a sub-set of the total skeletal biomolecules, those protected from exposure to a strong oxidising agent (NaOCl); the so-called intra-crystalline component. The extent of peptide bond hydrolysis was compared with the declining immunological signal. The proportion of free amino acids increased very rapidly but between 5 and 10% of the amino acids remained peptide bound in all samples. The pattern of loss of immunological reactivity broadly mirrored the loss of peptide bonds, but overall loss of signal was much greater. Significant antibody response was observed in some but not all late Pliocene fossils (>3 Ma), but against a panel of antisera the pattern of reactivity was lost in samples >0.5 Ma. Alternative models of polypeptide chain scission were used in an to attempt to relate the rate of peptide bond hydrolysis to the loss of immunological determinants. The findings suggest that, despite early optimistic reports, the application of immunology to shell carbonates does not appear capable of extending into deep time.

A Method for Conducting Simultaneous Convergent Tracer Tests in Multilayered Aquifers

Forced gradient tracer tests between two boreholes can be used to study contaminant transport processes at the small field scale or investigate the transport properties of an aquifer. Full depth tests, in which tracer samples are collected just from the discharge of the abstraction borehole, often give rise to breakthrough curves with multiple peaks that are usually attributed to different flow paths through the aquifer that can rarely be identified from the test results alone. Tests in selected levels of the aquifer, such as those between packer-isolated sections of the boreholes, are time consuming, expensive; and the identification of major transport pathways is not guaranteed. We present a method for simultaneously conducting multiple tracer tests covering the full depth of the boreholes, in which tracer sampling and monitoring is carried out by a novel multilevel sampling system allowing high frequency and cumulative sampling options. The method is applied to a tracer test using fluorescein conducted in the multilayered sandstone aquifer beneath the city of Birmingham, UK, producing six well-defined tracer breakthrough curves.

Development of a Methodology to Quantify the Importance of Hydro-Mechanical Processes in Radionuclide Migration Assessments

Abstract A methodology for quantifying the contributions of hydro-mechanical processes to fractured rock hydraulic property distributions has been developed and tested. Simulations have been carried out on discrete fracture networks to study the sensitivity of hydraulic properties to mechanical properties, stress changes with depth, mechanical boundary conditions, initial mechanical apertures and fracture network geometry. The results indicate that the most important (and uncertain) parameters for modelling HM processes in fractured rock are fracture density and rock/fracture mechanical properties. Aperture variation with depth below ground surface is found to be of second order importance.

Understanding the Impact of Hydro-Mechanical Coupling on Performance Assessment of Deep Waste Disposal

Abstract A methodology for understanding the importance of modelling hydro-mechanical (HM) processes in performance assessment of a radioactive waste site in fractured rock has been established. Results of HM-modelling performed with UDEC-BB, the universal distinct element code incorporating the empirical Barton-Bandis model, revealed large variations in hydraulic aperture distribution depending on the applied mechnical properties and the stress conditions. Continuum modelling was undertaken using mean upscaled hydraulic conductivity and porosity values for two cases - a hydraulic only analysis and a hydro-mechanical analysis for a hypothetical repository setting. The modelling of these cases showed that the most significant HM factors for performance assessment at the regional scale are the aperture distributions that depend on the variations and the spatial distribution of the mechanical properties. Uncertainties in the fracture density and the spatial distribution of different fracture densities appear to be less important than knowledge of the mechanical properties.