Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries

The extraordinary potential of metagenomic functional analyses to identify activities of interest present in uncultured microorganisms has been limited by reduced gene expression in surrogate hosts. We have developed vectors and specialized E. coli strains as improved metagenomic DNA heterologous expression systems, taking advantage of viral components that prevent transcription termination at metagenomic terminators. One of the systems uses the phage T7 RNA-polymerase to drive metagenomic gene expression, while the other approach uses the lambda phage transcription anti-termination protein N to limit transcription termination. A metagenomic library was constructed and functionally screened to identify genes conferring carbenicillin resistance to E. coli. The use of these enhanced expression systems resulted in a 6-fold increase in the frequency of carbenicillin resistant clones. Subcloning and sequence analysis showed that, besides β-lactamases, efflux pumps are not only able contribute to carbenicillin resistance but may in fact be sufficient by themselves to convey carbenicillin resistance.España, Ministerio de Educación y Ciencia BIO2011-24003España, Ministerio de Educación y Ciencia CSD2007-000

Measurement of event shapes in deep inelastic scattering at HERA

Inclusive event-shape variables have been measured in the current region of the Breit frame for neutral current deep inelastic ep scattering using an integrated luminosity of 45.0 pb^-1 collected with the ZEUS detector at HERA. The variables studied included thrust, jet broadening and invariant jet mass. The kinematic range covered was 10 < Q^2 < 20,480 GeV^2 and 6.10^-4 < x < 0.6, where Q^2 is the virtuality of the exchanged boson and x is the Bjorken variable. The Q dependence of the shape variables has been used in conjunction with NLO perturbative calculations and the Dokshitzer-Webber non-perturbative corrections (`power corrections') to investigate the validity of this approach.Comment: 7+25 pages, 6 figure

Observation of isolated high-E_T photons in deep inelastic scattering

First measurements of cross sections for isolated prompt photon production in deep inelastic ep scattering have been made using the ZEUS detector at the HERA electron-proton collider using an integrated luminosity of 121 pb^-1. A signal for isolated photons in the transverse energy and rapidity ranges 5 < E_T^gamma < 10 GeV and -0.7 < eta^gamma < 0.9 was observed for virtualities of the exchanged photon of Q^2 > 35 GeV^2. Cross sections are presented for inclusive prompt photons and for those accompanied by a single jet in the range E_T^jet \geq 6 GeV and -1.5 \leq eta^jet < 1.8. Calculations at order alpha^3alpha_s describe the data reasonably well.Comment: 16 pages, 5 figure

Measurement of beauty production in deep inelastic scattering at HERA

The beauty production cross section for deep inelastic scattering events with at least one hard jet in the Breit frame together with a muon has been measured, for photon virtualities Q^2 > 2 GeV^2, with the ZEUS detector at HERA using integrated luminosity of 72 pb^-1. The total visible cross section is sigma_b-bbar (ep -> e jet mu X) = 40.9 +- 5.7 (stat.) +6.0 -4.4 (syst.) pb. The next-to-leading order QCD prediction lies about 2.5 standard deviations below the data. The differential cross sections are in general consistent with the NLO QCD predictions; however at low values of Q^2, Bjorken x, and muon transverse momentum, and high values of jet transverse energy and muon pseudorapidity, the prediction is about two standard deviations below the data.Comment: 18 pages, 4 figure

Photoproduction of D∗±D^{*\pm} mesons associated with a leading neutron

The photoproduction of $D^{*\pm} (2010)$ mesons associated with a leading neutron has been observed with the ZEUS detector in $ep$ collisions at HERA using an integrated luminosity of 80 pb$^{-1}$. The neutron carries a large fraction, {$x_L>0.2$}, of the incoming proton beam energy and is detected at very small production angles, {$\theta_n<0.8$ mrad}, an indication of peripheral scattering. The $D^*$ meson is centrally produced with pseudorapidity {$|\eta| 1.9$ GeV}, which is large compared to the average transverse momentum of the neutron of 0.22 GeV. The ratio of neutron-tagged to inclusive $D^*$ production is $8.85\pm 0.93({\rm stat.})^{+0.48}_{-0.61}({\rm syst.})\%$ in the photon-proton center-of-mass energy range {$130 <W<280$ GeV}. The data suggest that the presence of a hard scale enhances the fraction of events with a leading neutron in the final state.Comment: 28 pages, 4 figures, 2 table

Search for contact interactions, large extra dimensions and finite quark radius in ep collisions at HERA

A search for physics beyond the Standard Model has been performed with high-Q^2 neutral current deep inelastic scattering events recorded with the ZEUS detector at HERA. Two data sets, e^+ p \to e^+ X and e^- p \to e^- X, with respective integrated luminosities of 112 pb^-1 and 16 pb^-1, were analyzed. The data reach Q^2 values as high as 40000 GeV^2. No significant deviations from Standard Model predictions were observed. Limits were derived on the effective mass scale in eeqq contact interactions, the ratio of leptoquark mass to the Yukawa coupling for heavy leptoquark models and the mass scale parameter in models with large extra dimensions. The limit on the quark charge radius, in the classical form factor approximation, is 0.85 10^-16 cm.Comment: 28 pages, 4 figures, accepted for publication in Physics Letters

Isolated tau leptons in events with large missing transverse momentum at HERA

A search for events containing isolated tau leptons and large missing transverse momentum, not originating from the tau decay, has been performed with the ZEUS detector at the electron-proton collider HERA, using 130 pb^-1 of integrated luminosity. A search was made for isolated tracks coming from hadronic tau decays. Observables based on the internal jet structure were exploited to discriminate between tau decays and quark- or gluon-induced jets. Three tau candidates were found, while 0.40 +0.12 -0.13 were expected from Standard Model processes, such as charged current deep inelastic scattering and single W-boson production. To search for heavy-particle decays, a more restrictive selection was applied to isolate tau leptons produced together with a hadronic final state with high transverse momentum. Two candidate events survive, while 0.20 +-0.05 events are expected from Standard Model processes.Comment: 28 pages, 4 figures, 3 tables, accepted by Phys. Lett. B. Updated with minor changes to the text requested by the journal refere

Forward jet production in deep inelastic ep scattering and low-x parton dynamics at HERA

Differential inclusive jet cross sections in neutral current deep inelastic ep scattering have been measured with the ZEUS detector. Three phase-space regions have been selected in order to study parton dynamics where the effects of BFKL evolution might be present. The measurements have been compared to the predictions of leading-logarithm parton shower Monte Carlo models and fixed-order perturbative QCD calculations. In the forward region, QCD calculations at order alpha_s^1 underestimate the data up to an order of magnitude at low x. An improved description of the data in this region is obtained by including QCD corrections at order alpha_s^2, which account for the lowest-order t-channel gluon-exchange diagrams, highlighting the importance of such terms in parton dynamics at low x.Comment: 25 pages, 4 figure

Estimation of neutron-equivalent dose in organs of patients undergoing radiotherapy by the use of a novel online digital detector.

Neutron peripheral contamination in patients undergoing high-energy photon radiotherapy is considered as a risk factor for secondary cancer induction. Organ-specific neutron-equivalent dose estimation is therefore essential for a reasonable assessment of these associated risks. This work aimed to develop a method to estimate neutron-equivalent doses in multiple organs of radiotherapy patients. The method involved the convolution, at 16 reference points in an anthropomorphic phantom, of the normalized Monte Carlo neutron fluence energy spectra with the kerma and energy-dependent radiation weighting factor. This was then scaled with the total neutron fluence measured with passive detectors, at the same reference points, in order to obtain the equivalent doses in organs. The latter were correlated with the readings of a neutron digital detector located inside the treatment room during phantom irradiation. This digital detector, designed and developed by our group, integrates the thermal neutron fluence. The correlation model, applied to the digital detector readings during patient irradiation, enables the online estimation of neutron-equivalent doses in organs. The model takes into account the specific irradiation site, the field parameters (energy, field size, angle incidence, etc) and the installation (linac and bunker geometry). This method, which is suitable for routine clinical use, will help to systematically generate the dosimetric data essential for the improvement of current risk-estimation models

High-Q^2 neutral current cross sections in e^+p deep inelastic scattering at sqrt{s}=318 GeV

Cross sections for e^+p neutral current deep inelastic scattering have been measured at a centre-of-mass energy of sqrt{s}=318 GeV with the ZEUS detector at HERA using an integrated luminosity of 63.2 pb^-1. The double-differential cross section, d^2sigma/dxdQ^2, is presented for 200 GeV^2 < Q^2 < 30000 GeV^2 and for 0.005 < x < 0.65. The single-differential cross-sections dsigma/dQ^2, dsigma/dx and dsigma/dy are presented for Q^2 > 200 GeV^2. The effect of Z-boson exchange is seen in dsigma/dx measured for Q^2 > 10000 GeV^2. The data presented here were combined with ZEUS e^+p neutral current data taken at sqrt{s}=300 GeV and the structure function F_2^{em} was extracted. All results agree well with the predictions of the Standard Model.Comment: Two references corrected. To be published in Physical Review