Simulating Wde-area Replication

We describe our experiences with simulating replication algorithms for use in far flung distributed systems. The algorithms under scrutiny mimic epidemics. Epidemic algorithms seem to scale and adapt to change (such as varying replica sets) well. The loose consistency guarantees they make seem more useful in applications where availability strongly outweighs correctness; e.g., distributed name service

Use of high throughput sequencing to observe genome dynamics at a single cell level

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions. Here, we sequenced several genomes of Escherichia coli from colonies obtained after chemical mutagenesis and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the genome and orders of magnitude intra- and inter-genomic differences in mutation density. Whereas most of these observations can be explained by the known features of enzymatic processes, the others could reflect stochasticity in the molecular processes at the single-cell level. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor.Comment: 22 pages, 9 figures (including 5 supplementary), one tabl

+SPACES: Serious Games for Role-Playing Government Policies

The paper explores how role-play simulations can be used to support policy discussion and refinement in virtual worlds. Although the work described is set primarily within the context of policy formulation for government, the lessons learnt are applicable to online learning and collaboration within virtual environments. The paper describes how the +Spaces project is using both 2D and 3D virtual spaces to engage with citizens to explore issues relevant to new government policies. It also focuses on the most challenging part of the project, which is to provide environments that can simulate some of the complexities of real life. Some examples of different approaches to simulation in virtual spaces are provided and the issues associated with them are further examined. We conclude that the use of role-play simulations seem to offer the most benefits in terms of providing a generalizable framework for citizens to engage with real issues arising from future policy decisions. Role-plays have also been shown to be a useful tool for engaging learners in the complexities of real-world issues, often generating insights which would not be possible using more conventional techniques

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds