Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing

Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.

Is there really "nothing you can do"? Pathways to enhanced flood-risk preparedness

Whilst policy makers have tended to adopt an ‘information-deficit model’ to bolster levels of flood-risk preparedness primarily though communication strategies promoting awareness, the assumed causal relation between awareness and preparedness is empirically weak. As such, there is a growing interest amongst scholars and policy makers alike to better understand why at-risk individuals are underprepared. In this vein, empirical studies, typically employing quantitative methods, have tended to focus on exploring the extent to which flood-risk preparedness levels vary depending not only on socio-demographic variables, but also (and increasingly so) the perceptual factors that influence flood risk preparedness. This study builds upon and extends this body of research by offering a more solution-focused approach that seeks to identify how pathways to flood-risk preparedness can be opened up. Specifically, through application of a qualitative methodology, we seek to explore how the factors that negatively influence flood-risk preparedness can be addressed to foster a shift towards greater levels of mitigation behaviour. In doing so, we focus our analysis on an urban community in Ireland that is identified as ‘at risk’ of flash flooding and is currently undergoing significant flood relief works. In this regard, the case study offers an interesting laboratory to explore how attitudes towards flood-risk preparedness at the individual level are being influenced within the context of a flood relief scheme that is only partially constructed. In order to redress the dearth of theoretically informed qualitative studies in this field, we draw on Protection Motivation Theory (PMT) to help guide our analysis and make sense of our results. Our findings demonstrate that flood-risk preparedness can be undermined by low levels of efficacy amongst individuals in terms of the preparedness measures available to them and their own personal capacity to implement them. We also elucidate that the ‘levee effect’ can occur before engineered flood defences are fully constructed as the flood relief works within our case study are beginning to affect people’s perception of flood risk in the case study area. We conclude by arguing that 1) individuals’ coping appraisals need to be enhanced through communication strategies and other interventions which highlight that future floods may not replicate past events; and 2) the concept of residual risk needs to be communicated at all stages of a flood relief scheme, not just upon completion.