Cloning, sequencing, and characterization of the hexahydro-1,3,5-trinitro-1,3,5-triazine degradation gene cluster from Rhodococcus rhodochrous

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive which presents an environmental hazard as a major land and groundwater contaminant. Rhodococcus rhodochrous strain 11Y was isolated from explosive contaminated land and is capable of degrading RDX when provided as the sole source of nitrogen for growth. Products of RDX degradation in resting-cell incubations were analyzed and found to include nitrite, formaldehyde, and formate. No ammonium was excreted into the medium, and no dead-end metabolites were observed. The gene responsible for the degradation of RDX in strain 11Y is a constitutively expressed cytochrome P450-like gene, xpLA, which is found in a gene cluster with an adrenodoxin reductase homologue, xplB. The cytochrome P450 also has a flavodoxin domain at the N terminus. This study is the first to present a gene which has been identified as being responsible for RDX biodegradation. The mechanism of action of XplA on RDX is thought to involve initial denitration followed by spontaneous ring cleavage and mineralization

Stellar populations across the NGC4244 truncated galactic disk

We use HST/ACS to study the resolved stellar populations of the nearby, nearly edge-on galaxy NGC4244 across its outer disk surface density break. The stellar photometry allows us to study the distribution of different stellar populations and reach very low equivalent surface brightnesses. We find that the break occurs at the same radius for young, intermediate age, and old stars. The stellar density beyond the break drops sharply by a factor of at least 600 in 5 kpc. The break occurs at the same radius independent of height above the disk, but is sharpest in the midplane and nearly disappears at large heights. These results make it unlikely that truncations are caused by a star formation threshold alone: the threshold would have to keep the same radial position from less than 100 Myr to 10 Gyr ago, in spite of potential disturbances such as infall and redistribution of gas by internal processes. A dynamical interpretation of truncation formation is more likely such as due to angular momentum redistribution by bars or density waves, or heating and stripping of stars caused by the bombardment of dark matter sub-halos. The latter explanation is also in quantitative agreement with the small diffuse component we see around the galaxy.Comment: ApJ Letters, in press. Five pages, 2 figure

ESBL displace: a protocol for an observational study to identify displacing Escherichia coli strain candidates from ESBL-colonized travel returners using phenotypic, genomic sequencing and metagenome analysis

Introduction: Invading extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-PE), non-ESBL E. coli, and other bacteria form a complex environment in the gut. The duration and dynamics of ESBL-PE colonization varies among individuals. Understanding the factors associated with colonization may lead to decolonization strategies. In this study, we aim to identify (i) single E. coli strains and (ii) microbiome networks that correlate with retention or decline of colonization, and (iii) pan-sensitive E. coli strains that potentially could be used to displace ESBL-PE during colonization. Methods and analysis: We recruit healthy travellers to Southeast Asia for a one-year prospective observational follow-up study. We collect and biobank stool, serum, and peripheral blood mononuclear cells (PBMCs) at predefined timepoints. Additional information is collected with questionnaires. We determine the colonization status with ESBL-PE and non-ESBL E. coli and quantify cell densities in stools and ratios over time. We characterize multiple single bacterial isolates per patient and timepoint using whole genome sequencing (WGS) and 16S/ITS amplicon-based and shotgun metagenomics. We determine phylogenetic relationships between isolates, antimicrobial resistance (AMR; phenotypic and genotypic), and virulence genes. We describe the bacterial and fungal stool microbiome alpha and beta diversity on 16S/ITS metagenomic data. We describe patterns in microbiome dynamics to identify features associated with protection or risk of ESBL-PE colonization. Ethics and dissemination: The study is registered (clinicaltrials.gov; NCT04764500 on 09/02/2019) and approved by the Ethics Committee (EKNZ project ID 2019-00044). We will present anonymized results at conferences and in scientific journals. Bacterial sequencing data will be shared via publicly accessible databases according to FAIR principles

Emergence of qualia from brain activity or from an interaction of proto-consciousness with the brain: which one is the weirder? Available evidence and a research agenda

This contribution to the science of consciousness aims at comparing how two different theories can explain the emergence of different qualia experiences, meta-awareness, meta-cognition, the placebo effect, out-of-body experiences, cognitive therapy and meditation-induced brain changes, etc. The first theory postulates that qualia experiences derive from specific neural patterns, the second one, that qualia experiences derive from the interaction of a proto-consciousness with the brain\u2019s neural activity. From this comparison it will be possible to judge which one seems to better explain the different qualia experiences and to offer a more promising research agenda

Observation of the Dalitz Decay Ds∗+→Ds+e+e−D_{s}^{*+} \to D_{s}^{+} e^{+} e^{-}

Using 586 $\textrm{pb}^{-1}$ of $e^{+}e^{-}$ collision data acquired at $\sqrt{s}=4.170$ GeV with the CLEO-c detector at the Cornell Electron Storage Ring, we report the first observation of $D_{s}^{*+} \to D_{s}^{+} e^{+} e^{-}$ with a significance of $5.3 \sigma$. The ratio of branching fractions \calB(D_{s}^{*+} \to D_{s}^{+} e^{+} e^{-}) / \calB(D_{s}^{*+} \to D_{s}^{+} \gamma) is measured to be $[ 0.72^{+0.15}_{-0.13} (\textrm{stat}) \pm 0.10 (\textrm{syst})]$, which is consistent with theoretical expectations

Measurement of the Decay Constant fDS+f_D{_S^+} using $D_S^+ --> ell^+ nu

We measure the decay constant fDs using the Ds -> l+ nu channel, where the l+ designates either a mu+ or a tau+, when the tau+ -> pi+ nu. Using both measurements we find fDs = 274 +-13 +- 7 MeV. Combining with our previous determination of fD+, we compute the ratio fDs/fD+ = 1.23 +- 0.11 +- 0.04. We compare with theoretical estimates.Comment: 6 pages postscript,also available through http://www.lns.cornell.edu/public/CLNS/2007

Measurement of Absolute Hadronic Branching Fractions of D Mesons and e^+ e^- --> D D-bar Cross Sections at the psi(3770)

Using 281 /pb of e^+ e^- collisions recorded at the psi(3770) resonance with the CLEO-c detector at CESR, we determine absolute hadronic branching fractions of charged and neutral D mesons using a double tag technique. Among measurements for three D^0 and six D^+ modes, we obtain reference branching fractions B(D^0 --> K^-pi^+) = (3.891 +- 0.035 +- 0.059 +- 0.035)% and B(D^+ --> K^-pi^+pi^+) = (9.14 +- 0.10 +- 0.16 +- 0.07)%, where the first uncertainty is statistical, the second is all systematic errors other than final state radiation (FSR), and the third is the systematic uncertainty due to FSR. We include FSR in these branching fractions by allowing for additional unobserved photons in the final state. Using an independent determination of the integrated luminosity, we also extract the cross sections sigma(e+e- --> D^0 D^0-bar) = (3.66+- 0.03 +- 0.06) nb and sigma(e+e- --> D^+ D^-) = (2.91+- 0.03 +- 0.05) nb at a center of mass energy, E_cm = 3774 +- 1 MeV.Comment: 47 pages, postscript also available through this http://www.lns.cornell.edu/public/CLNS/2007/, to be published in PRD, updated branching fractions using B(KS0 --> pi+ pi-) from PDG 2007, and updated text in response to the PRD reviewe

A Study of Exclusive Charmless Semileptonic B Decays and Extraction of |V_{ub}| at CLEO

We have studied semileptonic B decay to the exclusive charmless states pi, rho/omega, eta and eta' using the full 15.5 fb^-1 CLEO Upsilon(4S) sample, with measurements performed in subregions of phase space to minimize dependence on a priori knowledge of the form factors involved. We find total branching fractions B(B^0 -> pi^-l^+nu) = (1.37 +- 0.15_stat +- 0.11_sys) x 10^-4 and B(B^0 -> rho^- l^+ nu) = (2.93 +- 0.37_stat +- 0.37_sys) x 10^-4. We find evidence for B^+ -> eta' l^+ nu, with B(B^+ -> eta' l^+ nu) = (2.66 +- 0.80_stat +- 0.56_sys) x 10^-4 and 1.20 x 10^-4 eta' l^+ nu) < 4.46 x 10^-4 (90% CL). We also limit B(B^+ -> eta l^+ nu) < 1.01 x 10^-4 (90% CL). By combining our B -> pi l nu information with unquenched lattice calculations, we find |V_ub| = (3.6 +- 0.4 +- 0.2 +0.6 -0.4) x 10^-3, where the errors are statistical, experimental systematic, and theoretical systematic, respectively.Comment: 35 pages, 15 figures; revise

Measurement of Interfering K^*+K^- and K^*-K^+ Amplitudes in the Decay D^0 --> K^+K^-pi^0

We have studied the Cabibbo-suppressed decay mode D^0 into K^+ K^- pi^0 using a Dalitz plot technique and find the strong phase difference delta_D [defined as delta_(K*^- K^+) - delta_(K*^+ K^-)] = 332 degrees +- 8 degrees +- 11 degrees and relative amplitude r_D [defined as a_(K*^- K^+) / a_(K*^+ K^-)] = 0.52 +- 0.05 +- 0.04. This measurement indicates significant destructive interference between D^0 into K^+ (K^- pi^0)_K*^- and D^0 into K^- (K^+ pi^0)_K*^+ in the Dalitz plot region where these two modes overlap. This analysis uses 9.0 fb^(-1) of data collected at s^(1/2) of approximately 10.58 GeV with the CLEO III detector.Comment: 10 pages postscript,also available through http://www.lns.cornell.edu/public/CLNS/2006/, Submitted to Phys. Rev. D (Rapid Communications

Search for Radiative Decays of Upsilon(1S) into eta and eta'

We report on a search for the radiative decay of Upsilon(1S) to the pseudoscalar mesons eta and etaprime in 21.2 +/- 0.2 times 10^6 Upsilon(1S) decays collected with the CLEO III detector at the Cornell Electron Storage Ring (CESR). The eta meson was reconstructed in the three modes eta to gamma-gamma, eta to pi+pi-pi0 and eta to 3pi0. The etaprime meson was reconstructed in the mode etaprime to pi+ pi- eta with eta decaying through any of the above three modes, and also etaprime to gamma rho, where rho decays to pi^+ pi^-. Five out of the seven sub-modes are found to be virtually background-free. In four of them we find no signal candidates and in one Upsilon(1S) to gamma-etaprime, etaprime to pi+ pi- eta, eta to pi+pi-pi0 there are two good signal candidates, which is insufficient evidence to claim a signal. The other two sub-modes eta to gamma-gamma and etaprime to gamma rho are background limited, and show no excess of events in their signal regions. We combine the results from different channels and obtain upper limits at the 90% C.L. which are B(Upsilon(1S) to gamma eta) < 1.0 times 10^-6 and B(Upsilon(1S) to gamma etaprime) < 1.9 times 10^-6. Our limits are an order of magnitude tighter than the previous ones and below the predictions made by some theoretical models.Comment: 14 pages postscript,also available through http://www.lns.cornell.edu/public/CLNS/2007/, Submitted to PR