Crystallization and preliminary X-ray analysis of a D-alanyl-D-alanine ligase (EcDdlB) from Escherichia coli

A recombinant form of Escherichia coli DdlB (EcDdlB) has been prepared and cocrystallized with ADP and D-alanyl-D-alanine to represent the ternary complex of EcDdlB. Furthermore, EcDdlB has been cocrystallized under the same conditions with the ligands ATP and D-alanyl-D-alanine, representing the product-inhibited complex. The crystals belonged to space group P212121, with unit-cell parameters a = 53.0, b = 97.6, c = 109.5 Å and a = 51.2, b = 97.8, c = 110.1 Å, respectively, and both contained two molecules in the asymmetric unit. Complete data sets were collected to 1.5 and 1.4 Å resolution, respectively, from single crystals under cryogenic conditions using synchrotron radiation

Spatiotemporal variability in the O-18-salinity relationship of seawater across the tropical Pacific Ocean

The relationship between salinity and the stable oxygen isotope ratio of seawater (δ18Osw) is of utmost importance to the quantitative reconstruction of past changes in salinity from δ18O values of marine carbonates. This relationship is often considered to be uniform across water masses, but the constancy of the δ18Osw-salinity relationship across space and time remains uncertain, as δ18Osw responds to varying atmospheric vapor sources and pathways, while salinity does not. Here we present new δ18Osw-salinity data from sites spanning the tropical Pacific Ocean. New data from Palau, Papua New Guinea, Kiritimati, and Galápagos show slopes ranging from 0.09 ‰/psu in the Galápagos to 0.32‰/psu in Palau. The slope of the δ18Osw-salinity relationship is higher in the western tropical Pacific versus the eastern tropical Pacific in observations and in two isotope-enabled climate model simulations. A comparison of δ18Osw-salinity relationships derived from short-term spatial surveys and multiyear time series at Papua New Guinea and Galápagos suggests spatial relationships can be substituted for temporal relationships at these sites, at least within the time period of the investigation. However, the δ18Osw-salinity relationship varied temporally at Palau, likely in response to water mass changes associated with interannual El Niño–Southern Oscillation (ENSO) variability, suggesting nonstationarity in this local δ18Osw-salinity relationship. Applying local δ18Osw-salinity relationships in a coral δ18O forward model shows that using a constant, basinwide δ18Osw-salinity slope can both overestimate and underestimate the contribution of δ18Osw to carbonate δ18O variance at individual sites in the western tropical Pacific.We are grateful for the dedicated water samplers who enabled this research: Lori J. Bell and Gerda Ucharm of the Coral Reef Research Foundation, Palau; Rosa Maritza Motoche Gonzalez and the Fuerza Aerea Ecuatoriana, Santa Cruz, Galapagos, Ecuador; Taonateiti Kabiri and the students of Tennessee Primary School, London, Kiritimati; and the Manus Weather Observers, U.S. Department of Energy ARM Climate Research Facility, Manus, Papua New Guinea. We would like to thank the Galapagos National Park, the Kiritimati Ministry of Environment Lands and Agricultural Development for sample permits, and the Charles Darwin Research Station for logistical support. Funding sources for this work includes NSF-AGS-PF 1049664 to J.L.C., NSF P2C2-1203785 to K.M.C., J.L.C., and D.N. This research was also supported by the Office of Biological and Environment Research of the U.S. Department of Energy as part of the Atmospheric Radiation Measurement Climate Research Facility. Isotope data are available as supporting information associated with the manuscript. (1049664 - NSF-AGS-PF; P2C2-1203785 - NSF; Office of Biological and Environment Research of the U.S. Department of Energy as part of the Atmospheric Radiation Measurement Climate Research Facility

Deducing signaling pathways from parallel actions of arsenite and antimonite in human epidermal keratinocytes.

Inorganic arsenic oxides have been identified as carcinogens in several human tissues, including epidermis. Due to the chemical similarity between trivalent inorganic arsenic (arsenite) and antimony (antimonite), we hypothesized that common intracellular targets lead to similarities in cellular responses. Indeed, transcriptional and proteomic profiling revealed remarkable similarities in differentially expressed genes and proteins resulting from exposure of cultured human epidermal keratinocytes to arsenite and antimonite in contrast to comparisons of arsenite with other metal compounds. These data were analyzed to predict upstream regulators and affected signaling pathways following arsenite and antimonite treatments. A majority of the top findings in each category were identical after treatment with either compound. Inspection of the predicted upstream regulators led to previously unsuspected roles for oncostatin M, corticosteroids and ephrins in mediating cellular response. The influence of these predicted mediators was then experimentally verified. Together with predictions of transcription factor effects more generally, the analysis has led to model signaling networks largely accounting for arsenite and antimonite action. The striking parallels between responses to arsenite and antimonite indicate the skin carcinogenic risk of exposure to antimonite merits close scrutiny

Incidence, outcomes, and risk factors of pleural effusion in patients receiving dasatinib therapy for Philadelphia chromosome-positive leukemia.

Dasatinib, a second-generation BCR-ABL1 tyrosine kinase inhibitor, is approved for the treatment of chronic myeloid leukemia and Philadelphia chromosome-positive acute lymphoblastic leukemia, both as first-line therapy and after imatinib intolerance or resistance. While generally well tolerated, dasatinib has been associated with a higher risk for pleural effusions. Frequency, risk factors, and outcomes associated with pleural effusion were assessed in two phase 3 trials (DASISION and 034/Dose-optimization) and a pooled population of 11 trials that evaluated patients with chronic myeloid leukemia and Philadelphia chromosome-positive acute lymphoblastic leukemia treated with dasatinib (including DASISION and 034/Dose-optimization). In this largest assessment of patients across the dasatinib clinical trial program (N=2712), pleural effusion developed in 6-9% of patients at risk annually in DASISION, and in 5-15% of patients at risk annually in 034/Dose-optimization. With a minimum follow up of 5 and 7 years, drug-related pleural effusion occurred in 28% of patients in DASISION and in 33% of patients in 034/Dose-optimization, respectively. A significant risk factor identified for developing pleural effusion by a multivariate analysis was age. We found that overall responses to dasatinib, progression-free survival, and overall survival were similar in patients who developed pleural effusion and in patients who did not. clinicaltrials.gov identifier 00481247; 00123474

Orexin-Corticotropin-Releasing Factor Receptor Heteromers in the Ventral Tegmental Area as Targets for Cocaine

Release of the neuropeptides corticotropin-releasing factor (CRF) and orexin-A in the ventral tegmental area (VTA) play an important role in stress-induced cocaine-seeking behavior. We provide evidence for pharmacologically significant interactions between CRF and orexin-A that depend on oligomerization of CRF1 receptor (CRF1R) and orexin OX1 receptors (OX1R). CRF1R–OX1R heteromers are the conduits of a negative crosstalk between orexin-A and CRF as demonstrated in transfected cells and rat VTA, in which they significantly modulate dendritic dopamine release. The cocaine target σ1 receptor (σ1R) also associates with the CRF1R–OX1R heteromer. Cocaine binding to the σ1R–CRF1R–OX1R complex promotes a long-term disruption of the orexin-A–CRF negative crosstalk. Through this mechanism, cocaine sensitizes VTA cells to the excitatory effects of both CRF and orexin-A, thus providing a mechanism by which stress induces cocaine seeking

Superhumps in Cataclysmic Binaries. XXII. 1RXS J232953.9+062814

We report photometry of 1RXS J232953.9+062814, a recently discovered dwarf nova with a remarkably short 64.2-minute orbital period. In quiescence, the star's light curve is that of a double sinusoid, arising from the "ellipsoidal" distortion of the Roche-lobe-filling secondary. During superoutburst, common superhumps develop with a period 3-4% longer than P_orb. This indicates a mass ratio M_2/M_1=0.19+-0.02, a surprisingly large value in so compact a binary. This implies that the secondary star has a density 2-3 times higher than that of other short-period dwarf novae, suggesting a secondary enriched by H-burning prior to the common-envelope phase of evolution. We estimate i=50+-5 deg, M_1=0.63 (+0.12, -0.09) M_sol, M_2=0.12 (+0.03, -0.02) M_sol, R_2=0.121 (+0.010, -0.007) R_sol, and a distance to the binary of 180+-40 pc.Comment: PDF, 17 pages, 3 tables, 5 figures; accepted, in press, to appear June 2002, PASP; more info at http://cba.phys.columbia.edu

Discovery of a Transiting Planet Near the Snow-Line

In most theories of planet formation, the snow-line represents a boundary between the emergence of the interior rocky planets and the exterior ice giants. The wide separation of the snow-line makes the discovery of transiting worlds challenging, yet transits would allow for detailed subsequent characterization. We present the discovery of Kepler-421b, a Uranus-sized exoplanet transiting a G9/K0 dwarf once every 704.2 days in a near-circular orbit. Using public Kepler photometry, we demonstrate that the two observed transits can be uniquely attributed to the 704.2 day period. Detailed light curve analysis with BLENDER validates the planetary nature of Kepler-421b to >4 sigmas confidence. Kepler-421b receives the same insolation as a body at ~2AU in the Solar System and for a Uranian albedo would have an effective temperature of ~180K. Using a time-dependent model for the protoplanetary disk, we estimate that Kepler-421b's present semi-major axis was beyond the snow-line after ~3Myr, indicating that Kepler-421b may have formed at its observed location.Comment: 14 pages, 10 figures, 3 tables. Accepted in Ap

Validation of Twelve Small Kepler Transiting Planets in the Habitable Zone

We present an investigation of twelve candidate transiting planets from Kepler with orbital periods ranging from 34 to 207 days, selected from initial indications that they are small and potentially in the habitable zone (HZ) of their parent stars. Few of these objects are known. The expected Doppler signals are too small to confirm them by demonstrating that their masses are in the planetary regime. Here we verify their planetary nature by validating them statistically using the BLENDER technique, which simulates large numbers of false positives and compares the resulting light curves with the Kepler photometry. This analysis was supplemented with new follow-up observations (high-resolution optical and near-infrared spectroscopy, adaptive optics imaging, and speckle interferometry), as well as an analysis of the flux centroids. For eleven of them (KOI-0571.05, 1422.04, 1422.05, 2529.02, 3255.01, 3284.01, 4005.01, 4087.01, 4622.01, 4742.01, and 4745.01) we show that the likelihood they are true planets is far greater than that of a false positive, to a confidence level of 99.73% (3 sigma) or higher. For KOI-4427.01 the confidence level is about 99.2% (2.6 sigma). With our accurate characterization of the GKM host stars, the derived planetary radii range from 1.1 to 2.7 R_Earth. All twelve objects are confirmed to be in the HZ, and nine are small enough to be rocky. Excluding three of them that have been previously validated by others, our study doubles the number of known rocky planets in the HZ. KOI-3284.01 (Kepler-438b) and KOI-4742.01 (Kepler-442b) are the planets most similar to the Earth discovered to date when considering their size and incident flux jointly.Comment: 27 pages in emulateapj format, including tables and figures. To appear in The Astrophysical Journa

Superhumps in Cataclysmic Binaries. XXV. q_crit, epsilon(q), and Mass-Radius

We report on successes and failures in searching for positive superhumps in cataclysmic variables, and show the superhumping fraction as a function of orbital period. Basically, all short-period systems do, all long-period systems don't, and a 50% success rate is found at P_orb=3.1+-0.2 hr. We can use this to measure the critical mass ratio for the creation of superhumps. With a mass-radius relation appropriate for cataclysmic variables, and an assumed mean white-dwarf mass of 0.75 M_sol, we find a mass ratio q_crit=0.35+-0.02. We also report superhump studies of several stars of independently known mass ratio: OU Virginis, XZ Eridani, UU Aquarii, and KV UMa (= XTE J1118+480). The latter two are of special interest, because they represent the most extreme mass ratios for which accurate superhump measurements have been made. We use these to improve the epsilon(q) calibration, by which we can infer the elusive q from the easy-to-measure epsilon (the fractional period excess of P_superhump over P_orb). This relation allows mass and radius estimates for the secondary star in any CV showing superhumps. The consequent mass-radius law shows an apparent discontinuity in radius near 0.2 M_sol, as predicted by the disrupted magnetic braking model for the 2.1-2.7 hour period gap. This is effectively the "empirical main sequence" for CV secondaries.Comment: PDF, 45 pages, 9 tables, 12 figures; accepted, in press, to appear November 2005, PASP; more info at http://cba.phys.columbia.edu

A super-Earth-sized planet orbiting in or near the habitable zone around Sun-like star

We present the discovery of a super-earth-sized planet in or near the habitable zone of a sun-like star. The host is Kepler-69, a 13.7 mag G4V-type star. We detect two periodic sets of transit signals in the three-year flux time series of Kepler-69, obtained with the Kepler spacecraft. Using the very high precision Kepler photometry, and follow-up observations, our confidence that these signals represent planetary transits is >99.1%. The inner planet, Kepler-69b, has a radius of 2.24+/-0.4 Rearth and orbits the host star every 13.7 days. The outer planet, Kepler-69c, is a super-Earth-size object with a radius of 1.7+/-0.3 Rearth and an orbital period of 242.5 days. Assuming an Earth-like Bond albedo, Kepler-69c has an equilibrium temperature of 299 +/- 19 K, which places the planet close to the habitable zone around the host star. This is the smallest planet found by Kepler to be orbiting in or near habitable zone of a Sun-like star and represents an important step on the path to finding the first true Earth analog.Comment: Accepted for publication in the Astrophysical Journa