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

A Search For Star Formation in the Smith Cloud

Motivated by the idea that a subset of HVCs trace dark matter substructure in the Local Group, we search for signs of star formation in the Smith Cloud, a nearby ~2x10^6 Msun HVC currently falling into the Milky Way. Using GALEX NUV and WISE/2MASS NIR photometry, we apply a series of color and apparent magnitude cuts to isolate candidate O and B stars that are plausibly associated with the Smith Cloud. We find an excess of stars along the line of sight to the cloud, but not at a statistically significant level relative to a control region. The number of stars found in projection on the cloud after removing an estimate of the contamination by the Milky Way implies an average star formation rate surface density of 10^(-4.8 +/- 0.3) Msun yr^(-1) kpc^(-2), assuming the cloud has been forming stars at a constant rate since its first passage through the Milky Way ~70 Myr ago. This value is consistent with the star formation rate expected based on the average gas density of the cloud. We also discuss how the newly discovered star forming galaxy Leo P has very similar properties to the Smith Cloud, but its young stellar population would not have been detected at a statistically significant level using our method. Thus, we cannot yet rule out the idea that the Smith Cloud is really a dwarf galaxy.Comment: 9 pages, 7 figures, accepted for publication in MNRA

The bird: A pressure-confined explosion in the interstellar medium

The non-thermal radio continuum source G5.3-1.0, mapped at 20 cm with the Very Large Array (VLA) by Becker and Helfand, has an unusual bird-like shape. In order to determine possible interaction of this source with adjacent cold gas, we have mapped this region in the J=1-0 line of CO using the AT and T Bell Laboratories 7m antenna and the FCRAO 14m antenna. The map shown contains 1859 spectra sampled on a 1.5 arcminute grid; each spectrum has an rms noise of 0.2 K in 1 MHz channels. There are several molecular clouds at different velocities along the line of sight. The outer regions of a previously unknown Giant Molecular Cloud (GMC) at l=4.7 deg., b=-0.85 deg., v=200 km s(-1) appears to be interacting with G5.3-10: the molecular cloud has a bird-shaped hole at the position of the continuum source, except that the brightest continuum point (the bird's head) appears to be embedded in the cloud. The velocity of this GMC indicates it is within 2 kpc of the galactic center. The morphology suggests that a supernova or other explosive event occurred near the outside of the GMC, in a region where (n) is approximately 300 cm(-3), and expanded into a region of lower density and pressure. The pressures, densities, and velocity gradients of molecular clouds near the galactic center are on average higher than those of clouds near the Sun. We therefore expect that Type II supernovae near the galactic center would be distorted by their interactions with their parent molecular clouds

Discovery of the Orbit of the Transient X ray Pulsar SAX J2103.5+4545

Using X-ray data from the Rossi X-Ray Timing Explorer (RXTE), we carried out pulse timing analysis of the transient X-ray pulsar SAX J2103.5+4545. An outburst was detected by All Sky Monitor (ASM) October 25 1999 and reached a peak X-ray brightness of 27 mCrab October 28. Between November 19 and December 27, the RXTE/PCA carried out pointed observations which provided us with pulse arrival times. These yield an eccentric orbit (e= 0.4 \pm 0.2) with an orbital period of 12.68 \pm 0.25 days and light travel time across the projected semimajor axis of 72 \pm 6 sec. The pulse period was measured to be 358.62171 \pm 0.00088 s and the spin-up rate (2.50 \pm 0.15) \times 10^{-13} Hz s^{-1}. The ASM data for the February to September 1997 outburst in which BeppoSAX discovered SAX J2103.5+4545 (Hulleman, in't Zand and Heise 1998) are modulated at time scales close to the orbital period. Folded light curves of the 1997 ASM data and the 1999 PCA data are similar and show that the intensity increases at periastron passages.Comment: To appear in The Astrophysical Journal (Letters

On measuring alpha in B(t)-> rho^\pm pi^\mp

Defining a most economical parametrization of time-dependent B-> rho^\pm pi^\mp decays, including a measurable phase alpha_{eff} which equals the weak phase alpha in the limit of vanishing penguin amplitudes, we propose two ways for determining alpha in this processes. We explain the limitation of one method, assuming only that two relevant tree amplitudes factorize and that their relative strong phase, delta_t, is negligible. The other method, based on broken flavor SU(3), permits a determination of alpha in B^0-> rho^\pm pi^\mp in an overconstrained system using also rate measurements of B^{0,+}-> K^* pi and B^{0,+}->rho K. Current data are shown to restrict two ratios of penguin and tree amplitudes, r_\pm, to a narrow range around 0.2, and to imply an upper bound |alpha_{eff} - alpha| < 15 degrees. Assuming that delta_t is much smaller than 90 degrees, we find alpha =(93\pm 16) degrees and (102 \pm 20) degrees using BABAR and BELLE results for B(t)-> rho^\pm pi^mp. Avoiding this assumption for completeness, we demonstrate the reduction of discrete ambiguities in alpha with increased statistics, and show that SU(3) breaking effects are effectively second order in r_\pm.Comment: 23 pages, 2 figures, data and references updated, to be published in Phys. Rev.

Evaluation of the in vitro Antiprotozoal Activity of Various Dry Plant Extracts against Dientamoeba fragilis

Plants represent an important source of diverse biomolecules with unique properties, some of which make them attractive candidates for the development of novel antimicrobials. Plant extracts have been evaluated in vitro for their activity against human-infecting gastrointestinal protozoa, such as Giardia intestinalis [1] and Entamoeba histolytica [2], with some success. Some plant extracts are also active against the sexually transmitted parasite Trichomonas vaginalis [2]