An assessment of the potential for in situ preservation of buried organic archaeological remains at Sutton Common, South Yorkshire

The broad aim of this research was to develop a methodological approach to the monitoring of archaeological sites that contained, or had the potential to contain, well-preserved organic archaeological remains, by means of a multidisciplinary approach. Such sites could generally be referred to as wetland archaeological sites, as material is preserved as a function of an existing or former wetland environment. Such an approach would provide high quality data from different sources that could be considered mutually supportive, generating information that could therefore be considered reliable. The more specific aims of the research can be considered as:1. To develop a monitoring package that can effectively and accurately identify conditions that are conducive to the long-term preservation of organic archaeological materials, specifically wood.2. To understand in detail the burial dynamics of Sutton Common.3. To identify the changes within the burial environment on Sutton Common that occurred as a direct consequence of activities aimed at raising the watertable and to assess whether these aided the potential for in situ preservation.Of significance is the amount and quality of the data collected, with the techniques used generating high resolution data over an extended period of time. Such data concerning the burial environment has not previously been collated to such an extent.To satisfy these three specific aims, a monitoring approach was chosen that made use of multiple factors; these being hydrological monitoring, soil redox monitoring and microbiological assessment. The most crucial of these, and the one that has been the focus of the monitoring effort, has been the hydrological monitoring as this is essential at identifying saturated conditions, which are the basic conditions required for good preservation. Soil redox monitoring closely supported this by being capable of identifying anaerobic conditions that indicate stable conditions, ideal for preservation. As soil redox monitoring requires more resources in terms of time and funds, this variable has not been as widely implemented as the piezometer grid installed for hydrological monitoring. Such factors have also influenced the implementation of microbial techniques on Sutton Common, with these being applied as an assessment, and a means of gathering baseline data, rather than a monitoring variable proper.The presentation of these techniques and the specific methods used have been detailed in Chapter 3, with the results of the monitoring programme for each of the approaches being presented in Chapters 5, 6 and 7 in the context of previous monitoring exercises and published literature. The significant findings were discussed and specific reference made to the impact of flooding on Sutton Common and the influence of re-wetting activities in Chapter 8.The concluding chapter summarises the main findings of each of the three disciplines studied along with the findings obtained from the analysis of the flooding event of 2000/01, and the effects of the drainage mitigation implemented on Sutton Common. These are then related to the original aims set out in Chapter 1, followed by the wider implications of this research and the main recommendations arising from it

Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics

Background
High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures. 
Results
We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.
Conclusions
Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.
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Science-based conservation and management in wetland archaeology: the example of Sutton Common, UK

Reproduced with permission of the publisher. © Oxbow Books and the individual auhtors, 2001. Details of the publication are available at: http://www.oxbowbooks.com/bookinfo.cfm/ID/3080