Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding was termed the recognition well. We find that there is recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations, and consider more rigorously the optimization of the orientations of the fragments about their long axes. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. However when torsional flexibility of the DNA molecules is introduced, we find excellent agreement between analytical approximation and simulation.Comment: Paper with supplemental material attached. 41 pages in all, 4 figures in main text, 3 figures in supplmental. To be submitted to Journa

Gender violence in schools: taking the ‘girls-as-victims’ discourse forward

This paper draws attention to the gendered nature of violence in schools. Recent recognition that schools can be violent places has tended to ignore the fact that many such acts originate in unequal and antagonistic gender relations, which are tolerated and ‘normalised’ by everyday school structures and processes. After examining some key concepts and definitions, we provide a brief overview of the scope and various manifestations of gender violence in schools, noting that most research to date has focused on girls as victims of gender violence within a heterosexual context and ignores other forms such as homophobic and girl violence. We then move on to look at a few interventions designed to address gender violence in schools in the developing world and end by highlighting the need for more research and improved understanding of the problem and how it can be addressed

Reconstructing the primordial power spectrum - a new algorithm

We propose an efficient and model independent method for reconstructing the primordial power spectrum from Cosmic Microwave Background (CMB) and large scale structure observations. The algorithm is based on a Monte Carlo principle and therefore very simple to incorporate into existing codes such as Markov Chain Monte Carlo. The algorithm has been used on present cosmological data to test for features in the primordial power spectrum. No significant evidence for features is found, although there is a slight preference for an overall bending of the spectrum, as well as a decrease in power at very large scales. We have also tested the algorithm on mock high precision CMB data, calculated from models with non-scale invariant primordial spectra. The algorithm efficiently extracts the underlying spectrum, as well as the other cosmological parameters in each case. Finally we have used the algorithm on a model where an artificial glitch in the CMB spectrum has been imposed, like the ones seen in the WMAP data. In this case it is found that, although the underlying cosmological parameters can be extracted, the recovered power spectrum can show significant spurious features, such as bending, even if the true spectrum is scale invariant.Comment: 22 pages, 12 figures, matches JCAP published versio

Precision mass measurements of magnesium isotopes and implications on the validity of the Isobaric Mass Multiplet Equation

If the mass excess of neutron-deficient nuclei and their neutron-rich mirror partners are both known, it can be shown that deviations of the Isobaric Mass Multiplet Equation (IMME) in the form of a cubic term can be probed. Such a cubic term was probed by using the atomic mass of neutron-rich magnesium isotopes measured using the TITAN Penning trap and the recently measured proton-separation energies of $^{29}$Cl and $^{30}$Ar. The atomic mass of $^{27}$Mg was found to be within 1.6$\sigma$ of the value stated in the Atomic Mass Evaluation. The atomic masses of $^{28,29}$Mg were measured to be both within 1$\sigma$, while being 8 and 34 times more precise, respectively. Using the $^{29}$Mg mass excess and previous measurements of $^{29}$Cl we uncovered a cubic coefficient of $d$ = 28(7) keV, which is the largest known cubic coefficient of the IMME. This departure, however, could also be caused by experimental data with unknown systematic errors. Hence there is a need to confirm the mass excess of $^{28}$S and the one-neutron separation energy of $^{29}$Cl, which have both come from a single measurement. Finally, our results were compared to ab initio calculations from the valence-space in-medium similarity renormalization group, resulting in a good agreement.Comment: 7 pages, 3 figure

Modulation of renal oxygenation and perfusion in rat kidney monitored by quantitative diffusion and blood oxygen level dependent magnetic resonance imaging on a clinical 1.5T platform

ARRIVE Checklist. (DOCX 42 kb

Some considerations concerning the challenge of incorporating social variables into epidemiological models of infectious disease transmission

Incorporation of ‘social’ variables into epidemiological models remains a challenge. Too much detail and models cease to be useful; too little and the very notion of infection —a highly social process in human populations—may be considered with little reference to the social. The French sociologist Emile Durkheim proposed that the scientific study of society required identification and study of ‘social currents.’ Such ‘currents’ are what we might today describe as ‘emergent properties,’ specifiable variables appertaining to individuals and groups, which represent the perspectives of social actors as they experience the environment in which they live their lives. Here we review the ways in which one particular emergent property, hope, relevant to a range of epidemiological situations, might be used in epidemiological modelling of infectious diseases in human populations. We also indicate how such an approach might be extended to include a range of other potential emergent properties to repre