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Article on an ab initio study of the ionization of sodium superoxide

Genome integration and excision by a new Streptomyces bacteriophage, ϕJoe

Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In Streptomyces, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here we present the genome of a new Streptomyces phage, ϕJoe, and investigate the conditions for integration and excision of the φJoe genome. ϕJoe belongs to the largest Streptomyces phage cluster (R4-like) and encodes a serine integrase. The attB site from S. venezuelae was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe int/attP locus. The attB site for ϕJoe integrase was occupied in several Streptomyces genomes, including S. coelicolor, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified and its function was confirmed in vivo Both the integrase and RDF were active in in vitro recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox. IMPORTANCE: Streptomyces spp. are prolific producers of secondary metabolites including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering as they enable integration of heterologous DNA into the Streptomyces chromosome with ease and high efficiency. Recently researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases we identified and validated the integrase from a newly isolated Streptomyces phage, ϕJoe. ϕJoe integrase is active in vitro and in vivo The specific recognition site for integration is present in a wide range of different Actinobacteria, including Streptomyces venezuelae, an emerging model bacterium in Streptomyces research

The role of fear-avoidance beliefs on low back pain-related disability in a developing socioeconomic and conservative culture : a cross-sectional study of a Pakistani population

Background: The relationship of low back pain, the world’s top disabling condition, with functional disability is often explained by the mediation effect of fear, catastrophizing, and psychological distress. These relationships have not been explored within chronic back pain patients from a low socio-economic, predominantly Muslim country. Thus, it was unclear whether previously established pathways would be consistent in Pakistani pain patients to help guide Pakistani clinicians caring for back pain patients. This cross-sectional study translated English versions of questionnaires within the fear-avoidance model into Urdu, tested the clini-metric properties of the Urdu versions for people with chronic low back pain (CLBP) in Pakistan, and performed mediation analysis to investigate pathways of the fear-avoidance model. Methods: Translation of questionnaires was completed in 4 steps using the forward-backward technique, with subsequent analyses for internal consistency (Cronbach’s α), construct validity (Pearson’s r-value), and test–retest reliability (ICC r-value). Multiple mediation analysis with bootstrapping was performed to analyze pathways within the fear-avoidance model from the Urdu translated questionnaires. Results: A total of 151 people from Pakistan with CLBP completed the questionnaires, with good results for internal consistency (r > 0.85), convergent validity (r > 0.59), and test–retest reliability (ICC r > 0.85). The association of pain with disability was significant (B=2.36, r2 = 0.19, p = 0.19, p<0.001, and the indirect effect of the mediators explained 81% of pain intensity’s total effect on disability. All mediators, apart from physical activity-related fear-avoidance beliefs, were significant mediators of the effect of pain intensity on disability. Conclusion: The Urdu versions of the fear-avoidance questionnaires show good clini-metric properties for use in clinical settings and research in Pakistan. These analyses support existing data for the mediation effect of catastrophizing, psychological distress, and self-efficacy on pain-related disability, and extends these findings to suggest that fear about work may be more important in a relatively lower socioeconomic sample of pain patients

Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif

To establish a prophage state, the genomic DNA of temperate bacteriophages normally becomes integrated into the genome of their host bacterium by integrase-mediated, site-specific DNA recombination. Serine integrases catalyse a single crossover between an attachment site in the host (attB) and a phage attachment site (attP) on the circularized phage genome to generate the integrated prophage DNA flanked by recombinant attachment sites, attL and attR. Exiting the prophage state and entry into the lytic growth cycle requires an additional phage-encoded protein, the recombination directionality factor or RDF, to mediate recombination between attL and attR and excision of the phage genome. The RDF is known to bind integrase and switch its activity from integration (attP x attB) to excision (attL x attR) but its precise mechanism is unclear. Here, we identify amino acid residues in the RDF, gp3, encoded by the Streptomyces phage ϕC31 and within the ϕC31 integrase itself that affect the gp3:Int interaction. We show that residue substitutions in integrase that reduce gp3 binding adversely affect both excision and integration reactions. The mutant integrase phenotypes are consistent with a model in which the RDF binds to a hinge region at the base of the coiled-coil motif in ϕC31 integrase

Reductions in movement-associated fear are dependent upon graded exposure in chronic low back pain : an exploratory analysis of a modified 3-item fear hierarchy

Objective: To explore the effectiveness of a modified fear hierarchy on measuring improvements in movement-associated fear in chronic low back pain. Methods: A modified 3-item fear hierarchy was created and implemented based on principles of graded exposure. This study was an exploratory analysis of the modified 3-item fear hierarchy from a larger clinical trial data set. Both groups received pain education and exercise, either bodyweight or strength training. Both groups performed item one on the hierarchy, the squat. Only the strength training group performed item 2, the deadlift. Neither group performed item 3, the overhead press. Analysis of Covariance and stepwise linear regression were used to explore results. Results: Improvement in movement-associated fear was conditional upon graded exposure. Both groups improved in the squat movement (p ≤ 0.05), which both performed. Only the strength training group improved in the deadlift (p ≤ 0.01), and neither improved in the overhead press (p ≥ 0.05). Conclusion: Reductions in movement-associated fear are conditional upon graded exposure, based on the use of a novel modified 3-item fear hierarchy. Further research is needed to understand the utility of this tool in a patient-led approach to co-designing a graded exposure-based intervention

The Nature of the Molecular Environment within 5 pc of the Galactic Center

We present a detailed study of molecular gas in the central 10pc of the Galaxy through spectral line observations of four rotation inversion transitions of NH3 made with the VLA. Updated line widths and NH3(1,1) opacities are presented, and temperatures, column densities, and masses are derived. We examine the impact of Sgr A East on molecular material at the Galactic center and find that there is no evidence that the expansion of this shell has moved a significant amount of the 50 km/s GMC. The western streamer, however, shows strong indications that it is composed of material swept-up by the expansion of Sgr A East. Using the mass and kinematics of the western streamer, we calculate an energy of E=(2-9)x10^{51} ergs for the progenitor explosion and conclude that Sgr A East was most likely produced by a single supernova. The temperature structure of molecular gas in the central ~20pc is also analyzed in detail. We find that molecular gas has a ``two-temperature'' structure similar to that measured by Huttemeister et al. (2003a) on larger scales. The largest observed line ratios, however, cannot be understood in terms of a two-temperature model, and most likely result from absorption of NH3(3,3) emission by cool surface layers of clouds. By comparing the observed NH3 (6,6)-to-(3,3) line ratios, we disentangle three distinct molecular features within a projected distance of 2pc from Sgr A*. Gas associated with the highest line ratios shows kinematic signatures of both rotation and expansion. The southern streamer shows no significant velocity gradients and does not appear to be directly associated with either the circumnuclear disk or the nucleus. The paper concludes with a discussion of the line-of-sight arrangement of the main features in the central 10pc.Comment: 51 pages, 16 figures, accepted for publication in ApJ. Due to size limitations, some of the images have been cut from this version. A complete, color PS or PDF version can be downloaded from http://www.astro.columbia.edu/~herrnstein/NH3/paper

A mapping approach to synchronization in the "Zajfman trap": stability conditions and the synchronization mechanism

We present a two particle model to explain the mechanism that stabilizes a bunch of positively charged ions in an "ion trap resonator" [Pedersen etal, Phys. Rev. Lett. 87 (2001) 055001]. The model decomposes the motion of the two ions into two mappings for the free motion in different parts of the trap and one for a compressing momentum kick. The ions' interaction is modelled by a time delay, which then changes the balance between adjacent momentum kicks. Through these mappings we identify the microscopic process that is responsible for synchronization and give the conditions for that regime.Comment: 12 pages, 9 figures; submitted to Phys Rev

Molecular Tracers of the Central 12 pc of the Galactic Center

We have used the BIMA array to image the Galactic Center with a 19-pointing mosaic in HCN(1-0), HCO+(1-0), and H 42-alpha emission with 5 km/s velocity resolution and 13'' x 4'' angular resolution. The 5' field includes the circumnuclear ring (CND) and parts of the 20 and 50 km/s clouds. HCN(1-0) and HCO+ trace the CND and nearby giant molecular clouds while the H 42-alpha emission traces the ionized gas in Sgr A West. We find that the CND has a definite outer edge in HCN and HCO+ emission at ~45'' radius and appears to be composed of two or three distinct streams of molecular gas rotating around the nucleus. Outside the CND, HCN and HCO+ trace dense clumps of high-velocity gas in addition to optically thick emission from the 20 and 50 km/s clouds. A molecular ridge of compressed gas and dust, traced in NH3 emission and self-absorbed HCN and HCO+, wraps around the eastern edge of Sgr A East. Just inside this ridge are several arcs of gas which have been accelerated by the impact of Sgr A East with the 50 km/s cloud. HCN and HCO+ emission trace the extension of the northern arm of Sgr A West which appears to be an independent stream of neutral and ionized gas and dust originating outside the CND. Broad line widths and OH maser emission mark the intersection of the northern arm and the CND. Comparison to previous NH3 and 1.2mm dust observations shows that HCN and HCO+ preferentially trace the CND and are weaker tracers of the GMCs than NH3 and dust. We discuss possible scenarios for the emission mechanisms and environment at the Galactic center which could explain the differences in these images.Comment: 24 pages, including 17 figures; to appear in The Astrophysical Journa