A comparison of different pre-lysis methods and extraction kits for recovery of Stretococcus agalacticae (Lancefield group B Streptococcus) DNA from whole blood

Sub-optimal recovery of bacterial DNA from whole blood samples can limit the sensitivity of molecular assays to detect pathogenic bacteria. We compared 3 different pre-lysis protocols (none, mechanical pre-lysis and achromopeptidasepre-lysis) and 5 commercially available DNA extraction platforms for direct detection of Group B Streptococcus (GBS) in spiked whole blood samples, without enrichment culture. DNA was extracted using the QIAamp Blood Mini kit (Qiagen), UCP Pathogen Mini kit (Qiagen), QuickGene DNA Whole Blood kit S (Fuji), Speed Xtract Nucleic Acid Kit 200 (Qiagen) and MagNA Pure Compact Nucleic Acid Isolation Kit I (Roche Diagnostics Corp). Mechanical pre-lysis increased yields of bacterial genomic DNA by 51.3 fold (95% confidence interval; 31.6–85.1, p < 0.001) and pre-lysis with achromopeptidase by 6.1 fold (95% CI; 4.2–8.9, p < 0.001), compared with no pre-lysis. Differences in yield dueto pre-lysis were 2–3 fold larger than differences in yield between extraction methods. Including a pre-lysis step can improve the limits of detection of GBS using PCR or other molecular methods without need for culture.

Rabbits, stoats and the predator problem: Why a strong animal rights position need not call for human intervention to protect prey from predators

Animal rights positions face the ‘predator problem’: the suggestion that if the rights of nonhuman animals are to be protected, then we are obliged to interfere in natural ecosystems to protect prey from predators. Generally, rather than embracing this conclusion, animal ethicists have rejected it, basing this objection on a number of different arguments. This paper considers but challenges three such arguments, before defending a fourth possibility. Rejected are Peter Singer’s suggestion that interference will lead to more harm than good, Sue Donaldson and Will Kymlicka’s suggestion that respect for nonhuman sovereignty necessitates non-interference in normal circumstances, and Alasdair Cochrane’s solution based on the claim that predators cannot survive without killing prey. The possibility defended builds upon Tom Regan’s suggestion that predators, as moral patients but not moral agents, cannot violate the rights of their prey, and so the rights of the prey, while they do exist, do not call for intervention. This idea is developed by a consideration of how moral agents can be more or less responsible for a given event, and defended against criticisms offered by thinkers including Alasdair Cochrane and Dale Jamieson.

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.