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

Beltrami state in black-hole accretion disk: A magnetofluid approach

Using the magnetofluid unification framework, we show that the accretion disk plasma (embedded in the background geometry of a blackhole) can relax to a class of states known as the Beltrami-Bernoulli (BB) equilibria. Modeling the disk plasma as a Hall MHD system, we find that the space-time curvature can significantly alter the magnetic/velocity decay rate as we move away from the compact object; the velocity profiles in BB states, for example, deviate substantially from the predicted corresponding geodesic velocity profiles. These departures imply a rich interplay of plasma dynamics and general relativity revealed by examining the corresponding Bernoulli condition representing "homogeneity" of total energy. The relaxed states have their origin in the constraints provided by the two helicity invariants of Hall MHD. These helicities conspire to introduce a new oscillatory length scale into the system that is strongly influenced by relativistic and thermal effects.Comment: 8 figure

Anomalous isotopic predissociation in the F³Πu(v=1) state of O₂

Using a tunable, narrow-bandwidth vacuum-ultraviolet source based on third-harmonic generation from excimer-pumped dye-laser radiation, the F³Πu←X³Σg-(1,0)photoabsorption cross sections of ¹⁶O₂ and ¹⁸O₂ have been recorded in high resolution. Rotational analyses have been performed and the resultant F(v=1) term values fitted to the ³Π Hamiltonian of Brown and Merer [J. Mol. Spectrosc. 74, 488 (1979)]. A large rotationless isotope effect is observed in the F(v=1)predissociation, wherein the Lorentzian linewidth component for ¹⁸O₂ is a factor of ∼50 smaller than the corresponding ¹⁶O₂linewidth. This effect, a consequence of the nonadiabatic rotationless predissociation mechanism, is described using a coupled-channel treatment of the strongly Rydberg-valence-mixed 3Πu states. Significant J, e/f-parity, and sublevel dependencies observed in the isotopic F(v=1) rotational widths are found to derive from an indirect predissociation mechanism involving an accidental degeneracy with the E³Σ−u(v=3) level, itself strongly predissociated by ³Σ−u Rydberg-valence interactions, together with L-uncoupling (rotational) interactions between the Rydberg components of the F and E states. Transitions into the E(v=3) level are observed directly for the first time, specifically in the ¹⁸O₂ spectrumPartial support was provided by an NSF International Opportunities for Scientists and Engineers Program Grant No. INT-9513350, and Visiting Fellowships for G.S. and J.B.W. at the Australian National University

Decelerating microdynamics can accelerate macrodynamics in the voter model

For the voter model, we study the effect of a memory-dependent transition rate. We assume that the transition of a spin into the opposite state decreases with the time it has been in its current state. Counter-intuitively, we find that the time to reach a macroscopically ordered state can be accelerated by slowing-down the microscopic dynamics in this way. This holds for different network topologies, including fully-connected ones. We find that the ordering dynamics is governed by two competing processes which either stabilize the majority or the minority state. If the first one dominates, it accelerates the ordering of the system. The conclusions of this Letter are not restricted to the voter model, but remain valid to many other spin systems as well.Comment: See http://www.sg.ethz.ch for related publication

Anti-aliasing with stratified B-spline filters of arbitrary degree

A simple and elegant method is presented to perform anti-aliasing in raytraced images. The method uses stratified sampling to reduce the occurrence of artefacts in an image and features a B-spline filter to compute the final luminous intensity at each pixel. The method is scalable through the specification of the filter degree. A B-spline filter of degree one amounts to a simple anti-aliasing scheme with box filtering. Increasing the degree of the B-spline generates progressively smoother filters. Computation of the filter values is done in a recursive way, as part of a sequence of Newton-Raphson iterations, to obtain the optimal sample positions in screen space. The proposed method can perform both anti-aliasing in space and in time, the latter being more commonly known as motion blur. We show an application of the method to the ray casting of implicit procedural surfaces

Keck Spectroscopy of Faint 3<z<8 Lyman Break Galaxies:- Evidence for a Declining Fraction of Emission Line Sources In the Redshift Range 6<z<8

Using deep Keck spectroscopy of Lyman break galaxies selected from infrared imaging data taken with WFC3/IR onboard the Hubble Space Telescope, we present new evidence for a reversal in the redshift-dependent fraction of star forming galaxies with detectable Lyman alpha emission in the redshift range 6.3 < z < 8.8. Our earlier surveys with the DEIMOS spectrograph demonstrated a significant increase with redshift in the fraction of line emitting galaxies over the interval 4 < z < 6, particularly for intrinsically faint systems which dominate the luminosity density. Using the longer wavelength sensitivities of LRIS and NIRSPEC, we have targeted 19 Lyman break galaxies selected using recent WFC3/IR data whose photometric redshifts are in the range 6.3 < z < 8.8 and which span a wide range of intrinsic luminosities. Our spectroscopic exposures typically reach a 5-sigma sensitivity of < 50 A for the rest-frame equivalent width (EW) of Lyman alpha emission. Despite the high fraction of emitters seen only a few hundred million years later, we find only 2 convincing and 1 possible line emitter in our more distant sample. Combining with published data on a further 7 sources obtained using FORS2 on the ESO VLT, and assuming continuity in the trends found at lower redshift, we discuss the significance of this apparent reversal in the redshift-dependent Lyman alpha fraction in the context of our range in continuum luminosity. Assuming all the targeted sources are at their photometric redshift and our assumptions about the Lyman alpha EW distribution are correct, we would expect to find so few emitters in less than 1% of the realizations drawn from our lower redshift samples. Our new results provide further support for the suggestion that, at the redshifts now being probed spectroscopically, we are entering the era where the intergalactic medium is partially neutral.Comment: 8 pages, 5 figures, Accepted to ApJ 10/1/1