Alleviation of restriction by DNA condensation and non-specific DNA binding ligands

During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA. In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA. How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme. We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy the ‘naked’ DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA

StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI

The nucleoid-associated protein, StpA, of Escherichia coli binds non-specifically to double-stranded DNA (dsDNA) and apparently forms bridges between adjacent segments of the DNA. Such a coating of protein on the DNA would be expected to hinder the action of nucleases. We demonstrate that StpA binding hinders dsDNA cleavage by both the non-specific endonuclease, DNase I, and by the site-specific type I restriction endonuclease, EcoKI. It requires approximately one StpA molecule per 250–300 bp of supercoiled DNA and approximately one StpA molecule per 60–100 bp on linear DNA for strong inhibition of the nucleases. These results support the role of StpA as a nucleoid-structuring protein which binds DNA segments together. The inhibition of EcoKI, which cleaves DNA at a site remote from its initial target sequence after extensive DNA translocation driven by ATP hydrolysis, suggests that these enzymes would be unable to function on chromosomal DNA even during times of DNA damage when potentially lethal, unmodified target sites occur on the chromosome. This supports a role for nucleoid-associated proteins in restriction alleviation during times of cell stress

The Bayesian Spatial Bradley--Terry Model: Urban Deprivation Modeling in Tanzania

Identifying the most deprived regions of any country or city is key if policy makers are to design successful interventions. However, locating areas with the greatest need is often surprisingly challenging in developing countries. Due to the logistical challenges of traditional household surveying, official statistics can be slow to be updated; estimates that exist can be coarse, a consequence of prohibitive costs and poor infrastructures; and mass urbanisation can render manually surveyed figures rapidly out-of-date. Comparative judgement models, such as the Bradley--Terry model, offer a promising solution. Leveraging local knowledge, elicited via comparisons of different areas' affluence, such models can both simplify logistics and circumvent biases inherent to house-hold surveys. Yet widespread adoption remains limited, due to the large amount of data existing approaches still require. We address this via development of a novel Bayesian Spatial Bradley--Terry model, which substantially decreases the amount of data comparisons required for effective inference. This model integrates a network representation of the city or country, along with assumptions of spatial smoothness that allow deprivation in one area to be informed by neighbouring areas. We demonstrate the practical effectiveness of this method, through a novel comparative judgement data set collected in Dar es Salaam, Tanzania.Comment: 23 pages, 7 figures, to be published in the journal of the Royal Statistical Society: Series

Analysis of principal nested spheres

A general framework for a novel non-geodesic decomposition of high-dimensional spheres or high-dimensional shape spaces for planar landmarks is discussed. The decomposition, principal nested spheres, leads to a sequence of submanifolds with decreasing intrinsic dimensions, which can be interpreted as an analogue of principal component analysis. In a number of real datasets, an apparent one-dimensional mode of variation curving through more than one geodesic component is captured in the one-dimensional component of principal nested spheres. While analysis of principal nested spheres provides an intuitive and flexible decomposition of the high-dimensional sphere, an interesting special case of the analysis results in finding principal geodesics, similar to those from previous approaches to manifold principal component analysis. An adaptation of our method to Kendall’s shape space is discussed, and a computational algorithm for fitting principal nested spheres is proposed. The result provides a coordinate system to visualize the data structure and an intuitive summary of principal modes of variation, as exemplified by several datasets

Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.

A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible for MRSA infections worldwide, and those of different lineages carry unique Type I restriction-modification (RM) variants. We have identified the specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and ST239. We experimentally demonstrate that this RM system is sufficient to block horizontal gene transfer between clinically important MRSA, confirming the bioinformatic evidence that each lineage is evolving independently. Target sites are distributed randomly in S. aureus genomes, except in a set of large conjugative plasmids encoding resistance genes that show evidence of spreading between two successful MRSA lineages. This analysis of the identification and distribution of target sites explains evolutionary patterns in a pathogenic bacterium. We show that a lack of specific target sites enables plasmids to evade the Type I RM system thereby contributing to the evolution of increasingly resistant community and hospital MRSA

On the stationarity of linearly forced turbulence in finite domains

A simple scheme of forcing turbulence away from decay was introduced by Lundgren some time ago, the `linear forcing', which amounts to a force term linear in the velocity field with a constant coefficient. The evolution of linearly forced turbulence towards a stationary final state, as indicated by direct numerical simulations (DNS), is examined from a theoretical point of view based on symmetry arguments. In order to follow closely the DNS the flow is assumed to live in a cubic domain with periodic boundary conditions. The simplicity of the linear forcing scheme allows one to re-write the problem as one of decaying turbulence with a decreasing viscosity. Scaling symmetry considerations suggest that the system evolves to a stationary state, evolution that may be understood as the gradual breaking of a larger approximate symmetry to a smaller exact symmetry. The same arguments show that the finiteness of the domain is intimately related to the evolution of the system to a stationary state at late times, as well as the consistency of this state with a high degree of isotropy imposed by the symmetries of the domain itself. The fluctuations observed in the DNS for all quantities in the stationary state can be associated with deviations from isotropy. Indeed, self-preserving isotropic turbulence models are used to study evolution from a direct dynamical point of view, emphasizing the naturalness of the Taylor microscale as a self-similarity scale in this system. In this context the stationary state emerges as a stable fixed point. Self-preservation seems to be the reason behind a noted similarity of the third order structure function between the linearly forced and freely decaying turbulence, where again the finiteness of the domain plays an significant role.Comment: 15 pages, 7 figures, changes in the discussion at the end of section VI, formula (60) correcte

Classical and quantum ergodicity on orbifolds

We extend to orbifolds classical results on quantum ergodicity due to Shnirelman, Colin de Verdi\`ere and Zelditch, proving that, for any positive, first-order self-adjoint elliptic pseudodifferential operator P on a compact orbifold X with positive principal symbol p, ergodicity of the Hamiltonian flow of p implies quantum ergodicity for the operator P. We also prove ergodicity of the geodesic flow on a compact Riemannian orbifold of negative sectional curvature.Comment: 14 page

A Process for Co-Designing Educational Technology Systems for Refugee Children

There is a growing interest in the potential for technology to facilitate emergency education of refugee children. However, designing in this space requires knowledge of the displaced population and the contextual dynamics surrounding it. Design should therefore be informed by both existing research across relevant disciplines, and from the practical experience of those who are on the ground facing the problem in real life. This paper describes a process for designing appropriate technology for these settings. The process draws on literature from emergency education, student engagement and motivation, educational technology, and participatory design. We emphasise a thorough understanding of the problem definition, the nature of the emergency, and of socio-cultural aspects that can inform the design process. We describe how this process was implemented leading to the design of a digital learning space for children living in a refugee camp in Greece. This drew on involving different groups of participants such as social-workers, parents, and children