DOCKside - A Tool for Docking Atomic Molecular Structures into Low-Resolution Electron Microscopy Graphs

The process of cryo-electron microscopy allows scientists to view the complex structures of proteins as they bind and interact with one another. This process however, outputs low resolution noisy density maps which in their initial form are of little use. Through a process called docking, high resolution models of each of the interacting components can be fitted into these low resolution maps so that further study can occur. DOCKside allows users to interact with 3D representations of the proteins and of the electron density maps. Design was an initial concern. Related work was studied to better create a efficient solution to the problem. Different techniques for visualising the various components are implemented and discussed. Docking can also be performed manually using interactive graphics or automatically using a range of mathematically intensive algorithms. These too are detailed and discussed. Through user testing, a review is made as to how efficient the docking process is in producing meaningful and accurate data when compared to the automatically docked solutions

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Gluttony, excess, and the fall of the planter class in the British Caribbean

Food and rituals around eating are a fundamental part of human existence. They can also be heavily politicized and socially significant. In the British Caribbean, white slaveholders were renowned for their hospitality towards one another and towards white visitors. This was no simple quirk of local character. Hospitality and sociability played a crucial role in binding the white minority together. This solidarity helped a small number of whites to dominate and control the enslaved majority. By the end of the eighteenth century, British metropolitan observers had an entrenched opinion of Caribbean whites as gluttons. Travelers reported on the sumptuous meals and excessive drinking of the planter class. Abolitionists associated these features of local society with the corrupting influences of slavery. Excessive consumption and lack of self-control were seen as symptoms of white creole failure. This article explores how local cuisine and white creole eating rituals developed as part of slave societies and examines the ways in which ideas about hospitality and gluttony fed into the debates over slavery that led to the dismantling of slavery and the fall of the planter class