Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides

AbstractWe have determined the crystal structure of an active, hexameric fragment of the gene 4 helicase from bacteriophage T7. The structure reveals how subunit contacts stabilize the hexamer. Deviation from expected six-fold symmetry of the hexamer indicates that the structure is of an intermediate on the catalytic pathway. The structural consequences of the asymmetry suggest a “binding change” mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled to conformational changes in the ring that most likely accompany duplex unwinding. The structure of a complex with a nonhydrolyzable ATP analog provides additional evidence for this hypothesis, with only four of the six possible nucleotide binding sites being occupied in this conformation of the hexamer. This model suggests a mechanism for DNA translocation

Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub

Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products

Chi hotspots trigger a conformational change in the helicase-like domain of AddAB to activate homologous recombination

In bacteria, the repair of double-stranded DNA breaks is modulated by Chi sequences. These are recognised by helicase-nuclease complexes that process DNA ends for homologous recombination. Chi activates recombination by changing the biochemical properties of the helicase-nuclease, transforming it from a destructive exonuclease into a recombination-promoting repair enzyme. This transition is thought to be controlled by the Chi-dependent opening of a molecular latch, which enables part of the DNA substrate to evade degradation beyond Chi. Here, we show that disruption of the latch improves Chi recognition efficiency and stabilizes the interaction of AddAB with Chi, even in mutants that are impaired for Chi binding. Chi recognition elicits a structural change in AddAB that maps to a region of AddB which resembles a helicase domain, and which harbours both the Chi recognition locus and the latch. Mutation of the latch potentiates the change and moderately reduces the duration of a translocation pause at Chi. However, this mutant displays properties of Chi-modified AddAB even in the complete absence of bona fide hotspot sequences. The results are used to develop a model for AddAB regulation in which allosteric communication between Chi binding and latch opening ensures quality control during recombination hotspot recognition

Spitzer Analysis of HII Region Complexes in the Magellanic Clouds: Determining a Suitable Monochromatic Obscured Star Formation Indicator

HII regions are the birth places of stars, and as such they provide the best measure of current star formation rates (SFRs) in galaxies. The close proximity of the Magellanic Clouds allows us to probe the nature of these star forming regions at small spatial scales. We aim to determine the monochromatic IR band that most accurately traces the bolometric IR flux (TIR), which can then be used to estimate an obscured SFR. We present the spatial analysis, via aperture/annulus photometry, of 16 LMC and 16 SMC HII region complexes using the Spitzer IRAC and MIPS bands. UV rocket data and SHASSA H-alpha data are also included. We find that nearly all of the LMC and SMC HII region SEDs peak around 70um, from ~10 to ~400 pc from the central sources. As a result, the sizes of HII regions as probed by 70um is approximately equal to the sizes as probed by TIR (about 70 pc in radius); the radial profile of the 70um flux, normalized by TIR, is constant at all radii (70um ~ 0.45 TIR); the 1-sigma standard deviation of the 70um fluxes, normalized by TIR, is a lower fraction of the mean (0.05 to 0.12 out to ~220 pc) than the normalized 8, 24, and 160um normalized fluxes (0.12 to 0.52); and these results are invariant between the LMC and SMC. From these results, we argue that 70um is the most suitable IR band to use as a monochromatic obscured star formation indicator because it most accurately reproduces the TIR of HII regions in the LMC and SMC and over large spatial scales. We also explore the general trends of the 8, 24, 70, and 160um bands in the LMC and SMC HII region SEDs, radial surface brightness profiles, sizes, and normalized (by TIR) radial flux profiles. We derive an obscured SFR equation that is modified from the literature to use 70um luminosity, SFR(Mo/yr) = 9.7(0.7)x10^{-44} L(70)(ergs/s), which is applicable from 10 to 300 pc distance from the center of an HII region.Comment: 21 pages, 12 figures, 4 tables. Will be published in ApJ

Herbicide-resistant weeds : from research and knowledge to future needs

Synthetic herbicides have been used globally to control weeds in major field crops. This has imposed a strong selection for any trait that enables plant populations to survive and reproduce in the presence of the herbicide. Herbicide resistance in weeds must be minimized because it is a major limiting factor to food security in global agriculture. This represents a huge challenge that will require great research efforts to develop control strategies as alternatives to the dominant and almost exclusive practice of weed control by herbicides. Weed scientists, plant ecologists and evolutionary biologists should join forces and work towards an improved and more integrated understanding of resistance across all scales. This approach will likely facilitate the design of innovative solutions to the global herbicide resistance challenge

The Calibration of Monochromatic Far-Infrared Star Formation Rate Indicators

(Abridged) Spitzer data at 24, 70, and 160 micron and ground-based H-alpha images are analyzed for a sample of 189 nearby star-forming and starburst galaxies to investigate whether reliable star formation rate (SFR) indicators can be defined using the monochromatic infrared dust emission centered at 70 and 160 micron. We compare recently published recipes for SFR measures using combinations of the 24 micron and observed H-alpha luminosities with those using 24 micron luminosity alone. From these comparisons, we derive a reference SFR indicator for use in our analysis. Linear correlations between SFR and the 70 and 160 micron luminosity are found for L(70)>=1.4x10^{42} erg/s and L(160)>=2x10^{42} erg/s, corresponding to SFR>=0.1-0.3 M_sun/yr. Below those two luminosity limits, the relation between SFR and 70 micron (160 micron) luminosity is non-linear and SFR calibrations become problematic. The dispersion of the data around the mean trend increases for increasing wavelength, becoming about 25% (factor ~2) larger at 70 (160) micron than at 24 micron. The increasing dispersion is likely an effect of the increasing contribution to the infrared emission of dust heated by stellar populations not associated with the current star formation. The non-linear relation between SFR and the 70 and 160 micron emission at faint galaxy luminosities suggests that the increasing transparency of the interstellar medium, decreasing effective dust temperature, and decreasing filling factor of star forming regions across the galaxy become important factors for decreasing luminosity. The SFR calibrations are provided for galaxies with oxygen abundance 12+Log(O/H)>8.1. At lower metallicity the infrared luminosity no longer reliably traces the SFR because galaxies are less dusty and more transparent.Comment: 69 pages, 19 figures, 2 tables; accepted for publication on Ap

Development of Backscatter X-Ray Imaging Techniques for Space Vehicle Applications

This slide presentation reviews the development of backscatter x ray (BSX) imaging techniques to perform inspection of spacecraft components. The techniques are currently being enhanced to advance Non-Destructive Testing (NDT) methods for future space vehicle applications. The presentation includes an overview of x ray techniques, a description of current BSX applications used on the space shuttle, the development for Constellation applications, and the use of the system for foam applications

Initial Semantics for Strengthened Signatures

We give a new general definition of arity, yielding the companion notions of signature and associated syntax. This setting is modular in the sense requested by Ghani and Uustalu: merging two extensions of syntax corresponds to building an amalgamated sum. These signatures are too general in the sense that we are not able to prove the existence of an associated syntax in this general context. So we have to select arities and signatures for which there exists the desired initial monad. For this, we follow a track opened by Matthes and Uustalu: we introduce a notion of strengthened arity and prove that the corresponding signatures have initial semantics (i.e. associated syntax). Our strengthened arities admit colimits, which allows the treatment of the \lambda-calculus with explicit substitution.Comment: In Proceedings FICS 2012, arXiv:1202.317