Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network.

BACKGROUND:Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become 'model' species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutation during growth on two pentose-rich substrates by transcriptome analysis. RESULTS:Particular attention was given to CAZymes, metabolic pathways and transcription factors related to the plant biomass degradation. Genes coding for the main enzymes involved in plant biomass degradation were down-regulated at the beginning of the growth on CS and SBH. However, at a later time point, significant differences were found in the expression profiles of both mutants on CS compared to SBH. CONCLUSION:This study demonstrates the high complexity of the plant biomass degradation process by fungi, by showing that mutant strains with fairly straightforward phenotypes on pure mono- and polysaccharides, have much less clear-cut phenotypes and transcriptomes on crude plant biomass

Hadronic production of squark-squark pairs: The electroweak contributions

We compute the electroweak (EW) contributions to squark--squark pair production processes at the LHC within the framework of the Minimal Supersymmetric Standard Model (MSSM). Both tree-level EW contributions, of O(alpha_s alpha + alpha^2), and next-to-leading order (NLO) EW corrections, of O(alpha_s^2 alpha), are calculated. Depending on the flavor and chirality of the produced quarks, many interferences between EW-mediated and QCD-mediated diagrams give non-zero contributions at tree-level and NLO. We discuss the computational techniques and present an extensive numerical analysis for inclusive squark--squark production as well as for subsets and single processes. While the tree-level EW contributions to the integrated cross sections can reach the 20% level, the NLO EW corrections typically lower the LO prediction by a few percent.Comment: 36 pages, 18 figure

Explaining the t tbar forward-backward asymmetry without dijet or flavor anomalies

We consider new physics explanations of the anomaly in the top quark forward-backward asymmetry measured at the Tevatron, in the context of flavor conserving models. The recently measured LHC dijet distributions strongly constrain many otherwise viable models. A new scalar particle in the antitriplet representation of flavor and color can fit the t tbar asymmetry and cross section data at the Tevatron and avoid both low- and high-energy bounds from flavor physics and the LHC. An s-channel resonance in uc to uc scattering at the LHC is predicted to be not far from the current sensitivity. This model also predicts rich top quark physics for the early LHC from decays of the new scalar particles. Single production gives t tbar j signatures with high transverse momentum jet, pair production leads to t tbar j j and 4 jet final states.Comment: 7 pages, 6 figures; v2: notation clarified, references adde

Measurement of the antineutrino neutral-current elastic differential cross section

arXiv:1309.7257v1 [hep-ex

Heavy-light decay topologies as a new strategy to discover a heavy gluon

We study the collider phenomenology of the lightest Kaluza-Klein excitation of the gluon, G*, in theories with a warped extra dimension. We do so by means of a two-site effective lagrangian which includes only the lowest-lying spin-1 and spin-1/2 resonances. We point out the importance of the decays of G* to one SM plus one heavy fermion, that were overlooked in the previous literature. It turns out that, when kinematically allowed, such heavy-light decays are powerful channels for discovering the G*. In particular, we present a parton-level Montecarlo analysis of the final state Wtb that follows from the decay of G* to one SM top or bottom quark plus its heavy partner. We find that at \sqrt{s} = 7 TeV and with 10 fb^{-1} of integrated luminosity, the LHC can discover a KK gluon with mass in the range M_{G*} = (1.8 - 2.2) TeV if its coupling to a pair of light quarks is g_{G*qqbar} = (0.2-0.5) g_3. The same process is also competitive for the discovery of the top and bottom partners as well. We find, for example, that the LHC at \sqrt{s} = 7 TeV can discover a 1 TeV KK bottom quark with an integrated luminosity of (5.3 - 0.61) fb^{-1} for g_{G*qqbar} = (0.2-0.5) g_3.Comment: 36 pages, 13 figures. v2: a few typos corrected, comments added, version published in JHE

Hadronic production of bottom-squark pairs with electroweak contributions

We present the complete computation of the tree-level and the next-to-leading order electroweak contributions to bottom-squark pair production at the LHC. The computation is performed within the minimal supersymmetric extension of the Standard Model. We discuss the numerical impact of these contributions in several supersymmetric scenarios.Comment: 33 pages, v2: preprint numbers correcte

Supersymmetric top and bottom squark production at hadron colliders

The scalar partners of top and bottom quarks are expected to be the lightest squarks in supersymmetric theories, with potentially large cross sections at hadron colliders. We present predictions for the production of top and bottom squarks at the Tevatron and the LHC, including next-to-leading order corrections in supersymmetric QCD and the resummation of soft gluon emission at next-to-leading-logarithmic accuracy. We discuss the impact of the higher-order corrections on total cross sections and transverse-momentum distributions, and provide an estimate of the theoretical uncertainty due to scale variation and the parton distribution functions.Comment: 29 pages, 6 figure

Probing CP Violation with and without Momentum Reconstruction at the LHC

We study the potential to observe CP-violating effects in SUSY cascade decay chains at the LHC. We consider squark and gluino production followed by subsequent decays into neutralinos with a three-body leptonic decay in the final step. Asymmetries composed by triple products of momenta of the final state particles are sensitive to CP-violating effects. Due to large boosts these asymmetries can be difficult to observe at a hadron collider. We show that using all available kinematic information one can reconstruct the decay chains on an event-by-event basis even in the case of 3-body decays, neutrinos and LSPs in the final state. We also discuss the most important experimental effects like major backgrounds and momentum smearing due to finite detector resolution. We show that with 300 fb$^{-1}$ of collected data, CP violation may be discovered at the LHC for a wide range of the phase of the bino mass parameter $M_1$.Comment: Version accepted for publication in JHEP. Clarifications added on the assumptions used for plots. New references adde

Warped Radion Dark Matter

Warped scenarios offer an appealing solution to the hierarchy problem. We consider a non-trivial deformation of the basic Randall-Sundrum framework that has a KK-parity symmetry. This leads to a stable particle beyond the Standard Model, that is generically expected to be the first KK-parity odd excitation of the radion field. We consider the viability of the KK-radion as a DM candidate in the context of thermal and non-thermal production in the early universe. In the thermal case, the KK-radion can account for the observed DM density when the radion decay constant is in the natural multi-TeV range. We also explore the effects of coannihilations with the first KK excitation of the RH top, as well as the effects of radion-Higgs mixing, which imply mixing between the KK-radion and a KK-Higgs (both being KK-parity odd). The non-thermal scenario, with a high radion decay constant, can also lead to a viable scenario provided the reheat temperature and the radion decay constant take appropriate values, although the reheat temperature should not be much higher than the TeV scale. Direct detection is found to be feasible if the DM has a small (KK-parity odd) Higgs admixture. Indirect detection via a photon signal from the galactic center is an interesting possibility, while the positron and neutrino fluxes from KK-radion annihilations are expected to be rather small. Colliders can probe characteristic aspects of the DM sector of warped scenarios with KK-parity, such as the degeneracy between the radion and the KK-radion (DM) modes.Comment: 43 pages, 16 figures; added reference

A prospective study of hearing changes after beginning zidovudine or didanosine in HIV-1 treatment-naïve people

BACKGROUND: While hearing loss in HIV-infected people after beginning nucleoside reverse transcriptase inhibitors (NRTIs) has been reported, there have been no prospective studies that measured hearing changes longitudinally in treatment-naïve HIV-infected subjects following initiation of regimens containing NRTIs. The goal of this study was to conduct a prospective assessment of the contribution of zidovudine (ZDV) and didanosine (ddI) to hearing loss METHODS/DESIGN: A prospective observational pilot study to determine whether ZDV or ddI, alone or in combination, are associated with sensorineural hearing loss in HIV-infected persons. Changes in hearing levels at all frequencies and in low and high frequency pure tone averages were measured at baseline, 16, and 32 weeks after initiating antiretroviral therapy. DISCUSSION: Treatment with ZDV and ddI did not result in loss of hearing, even after taking into account noise exposure, immune status and age. The results of this prospective pilot study do not support the notion that treatment with nucleoside antiretrovirals damages hearing