Gated rotation mechanism of site-specific recombination by ϕC31 integrase

Integrases, such as that of the Streptomyces temperate bacteriophage ϕC31, promote site-specific recombination between DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA. ϕC31 integrase belongs to the serine recombinase family, a large group of structurally related enzymes with diverse biological functions. It has been proposed that serine integrases use a “subunit rotation” mechanism to exchange DNA strands after double-strand DNA cleavage at the two recombining att sites, and that many rounds of subunit rotation can occur before the strands are religated. We have analyzed the mechanism of ϕC31 integrase-mediated recombination in a topologically constrained experimental system using hybrid “phes” recombination sites, each of which comprises a ϕC31 att site positioned adjacent to a regulatory sequence recognized by Tn3 resolvase. The topologies of reaction products from circular substrates containing two phes sites support a right-handed subunit rotation mechanism for catalysis of both integrative and excisive recombination. Strand exchange usually terminates after a single round of 180° rotation. However, multiple processive “360° rotation” rounds of strand exchange can be observed, if the recombining sites have nonidentical base pairs at their centers. We propose that a regulatory “gating” mechanism normally blocks multiple rounds of strand exchange and triggers product release after a single round

Dynamic model of gene regulation for the lac operon

Gene regulatory network is a collection of DNA which interact with each other and with other matter in the cell. The lac operon is an example of a relatively simple genetic network and is one of the best-studied structures in the Escherichia coli bacteria. In this work we consider a deterministic model of the lac operon with a noise term, representing the stochastic nature of the regulation. The model is written in terms of a system of simultaneous first order differential equations with delays. We investigate an analytical and numerical solution and analyse the range of values for the parameters corresponding to a stable solution

Physical State of Molecular Gas in High Galactic Latitude Translucent Clouds

The rotational transitions of carbon monoxide (CO) are the primary means of investigating the density and velocity structure of the molecular interstellar medium. Here we study the lowest four rotational transitions of CO towards high-latitude translucent molecular clouds (HLCs). We report new observations of the J = (4-3), (2-1), and (1-0) transitions of CO towards eight high-latitude clouds. The new observations are combined with data from the literature to show that the emission from all observed CO transitions is linearly correlated. This implies that the excitation conditions which lead to emission in these transitions are uniform throughout the clouds. Observed 13CO/12CO (1-0) integrated intensity ratios are generally much greater than the expected abundance ratio of the two species, indicating that the regions which emit 12CO (1-0) radiation are optically thick. We develop a statistical method to compare the observed line ratios with models of CO excitation and radiative transfer. This enables us to determine the most likely portion of the physical parameter space which is compatible with the observations. The model enables us to rule out CO gas temperatures greater than 30K since the most likely high-temperature configurations are 1 pc-sized structures aligned along the line of sight. The most probable solution is a high density and low temperature (HDLT) solution. The CO cell size is approximately 0.01 pc (2000 AU). These cells are thus tiny fragments within the 100 times larger CO-emitting extent of a typical high-latitude cloud. We discuss the physical implications of HDLT cells, and we suggest ways to test for their existence.Comment: 19 pages, 13 figures, 2 tables, emulateapj To be published in The Astrophysical Journa

Synchronizing Sequencing Software to a Live Drummer

Copyright 2013 Massachusetts Institute of Technology. MIT allows authors to archive published versions of their articles after an embargo period. The article is available at

Abell 370: A Cluster with a Pronounced Triaxial Morphology

We here combine Sunyaev-Zel'dovich effect, X-ray observations and spectroscopic redshifts of member galaxies, to constrain the intrinsic three-dimensional shape of the galaxy cluster: Abell 370. The cluster turns out to be strongly elongated along the l.o.s., with two (or more) substructures in the process of merging. Spectroscopy further suggests that the process must be taking place at a small angle respect to the l.o.s.Comment: 7 pages, 2 figures. Contribution to the Proceedings of the COSPAR Scientific Assembly, E1.2 "Clusters of Galaxies: New Insights from XMM-Newton, Chandra and INTEGRAL", Paris (France), July 19-20, 2004. Accepted for publication in Advances in Space Researc

Systems Technology Laboratory (STL) compendium of utilities

Multipurpose programs, routines and operating systems are described. Data conversion and character string comparison subroutine are included. Graphics packages, and file maintenance programs are also included

51 Eri and GJ 3305: A 10-15 Myr old binary star system at 30 parsecs

Following the suggestion of Zuckerman et al. (2001, ApJ, 562, L87), we consider the evidence that 51 Eri (spectral type F0) and GJ 3305 (M0), historically classified as unrelated main sequence stars in the solar neighborhood, are instead a wide physical binary system and members of the young beta Pic moving group (BPMG). The BPMG is the nearest (d < 50 pc) of several groups of young stars with ages around 10 Myr that are kinematically convergent with the Oph-Sco-Cen Association (OSCA), the nearest OB star association. Combining SAAO optical photometry, Hobby-Eberly Telescope high-resolution spectroscopy, Chandra X-ray data, and UCAC2 catalog kinematics, we confirm with high confidence that the system is indeed extremely young. GJ 3305 itself exhibits very strong magnetic activity but has rapidly depleted most of its lithium. The 51 Eri/GJ 3305 system is the westernmost known member of the OSCA, lying 110 pc from the main subgroups. The system is similar to the BPMG wide binary HD 172555/CD -64d1208 and the HD 104237 quintet, suggesting that dynamically fragile multiple systems can survive the turbulent environments of their natal giant molecular cloud complexes, while still being imparted high dispersion velocities. Nearby young systems such as these are excellent targets for evolved circumstellar disk and planetary studies, having stellar ages comparable to that of the late phases of planet formation.Comment: 27 pages, 7 figures. Accepted for publication in the Astronomical Journal. For a version with high resolution figures, see http://www.astro.psu.edu/users/edf/51Eri.pd

Beyond ‘witnessing’: children’s experiences of coercive control in domestic violence and abuse

Children’s experiences and voices are underrepresented in academic literature and professional practice around domestic violence and abuse. The project ‘Understanding Agency and Resistance Strategies’ addresses this absence, through direct engagement with children. We present an analysis from interviews with 21 children in the United Kingdom (12 girls and 9 boys, aged 8-18 years), about their experiences of domestic violence and abuse, and their responses to this violence. These interviews were analysed using interpretive interactionism. Three themes from this analysis are presented: a) ‘Children’s experiences of abusive control’, which explores children’s awareness of controlling behaviour by the adult perpetrator, their experience of that control, and its impact on them; b) ‘Constraint’, which explores how children experience the constraint associated with coercive control in situations of domestic violence, and c) ‘Children as agents’ which explores children’s strategies for managing controlling behaviour in their home and in family relationships. The paper argues that, in situations where violence and abuse occurs between adult intimate partners, children are significantly impacted, and can be reasonably described as victims of abusive control. Recognising children as direct victims of domestic violence and abuse would produce significant changes in the way professionals respond to them, by 1) recognising children’s experience of the impact of domestic violence and abuse; 2) recognising children’s agency, undermining the perception of them as passive ‘witnesses’ or ‘collateral damage’ in adult abusive encounters; and 3) strengthening professional responses to them as direct victims, not as passive witnesses to violence

A unified evaluation of iterative projection algorithms for phase retrieval

Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free diffraction-limited imaging and the possibility of using radiation for which no lenses exist. The challenge of this imaging technique is transfered from the lenses to the algorithms. We evaluate these new computational ``instruments'' developed for the phase retrieval problem, and discuss acceleration strategies.Comment: 12 pages, 9 figures, revte