Biodegradative mechanism of the brown rot basidiomycete Gloeophyllum trabeum: evidence for an extracellular hydroquinone-driven fenton reaction

AbstractWe have identified key components of the extracellular oxidative system that the brown rot fungus Gloeophyllum trabeum uses to degrade a recalcitrant polymer, polyethylene glycol, via hydrogen abstraction reactions. G. trabeum produced an extracellular metabolite, 2,5-dimethoxy-1,4-benzoquinone, and reduced it to 2,5-dimethoxyhydroquinone. In the presence of 2,5-dimethoxy-1,4-benzoquinone, the fungus also reduced extracellular Fe3+ to Fe2+ and produced extracellular H2O2. Fe3+ reduction and H2O2 formation both resulted from a direct, non-enzymatic reaction between 2,5-dimethoxyhydroquinone and Fe3+. polyethylene glycol depolymerization by G. trabeum required both 2,5-dimethoxy-1,4-benzoquinone and Fe3+ and was completely inhibited by catalase. These results provide evidence that G. trabeum uses a hydroquinone-driven Fenton reaction to cleave polyethylene glycol. We propose that similar reactions account for the ability of G. trabeum to attack lignocellulose

Comparative Oncogenomic Analysis of Copy Number Alterations in Human and Zebrafish Tumors Enables Cancer Driver Discovery

The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs) are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs). Given the low degree of conserved synteny between fish and mammals, we reasoned that comparative analyses of CNAs from fish versus human MPNSTs would enable elimination of a large proportion of passenger mutations, especially on large CNAs. We established a list of orthologous genes between human and zebrafish, which includes approximately two-thirds of human protein-coding genes. For the subset of these genes found in human MPNST CNAs, only one quarter of their orthologues were co-gained or co-lost in zebrafish, dramatically narrowing the list of candidate cancer drivers for both focal and large CNAs. We conclude that zebrafish-human comparative analysis represents a powerful, and broadly applicable, tool to enrich for evolutionarily conserved cancer drivers.Kathy and Curt Marble Cancer Research FundArthur C. MerrillNational Institutes of Health (U.S.) (Grant CA106416)National Institutes of Health (U.S.) (Grant ROI RR020833)National Institutes of Health (U.S.) (Grant 1F32GM095213-01

Fixation durations in scene viewing:Modeling the effects of local image features, oculomotor parameters, and task

Scene perception requires the orchestration of image- and task-related processes with oculomotor constraints. The present study was designed to investigate how these factors influence how long the eyes remain fixated on a given location. Linear mixed models (LMMs) were used to test whether local image statistics (including luminance, luminance contrast, edge density, visual clutter, and the number of homogeneous segments), calculated for 1° circular regions around fixation locations, modulate fixation durations, and how these effects depend on task-related control. Fixation durations and locations were recorded from 72 participants, each viewing 135 scenes under three different viewing instructions (memorization, preference judgment, and search). Along with the image-related predictors, the LMMs simultaneously considered a number of oculomotor and spatiotemporal covariates, including the amplitudes of the previous and next saccades, and viewing time. As a key finding, the local image features around the current fixation predicted this fixation’s duration. For instance, greater luminance was associated with shorter fixation durations. Such immediacy effects were found for all three viewing tasks. Moreover, in the memorization and preference tasks, some evidence for successor effects emerged, such that some image characteristics of the upcoming location influenced how long the eyes stayed at the current location. In contrast, in the search task, scene processing was not distributed across fixation durations within the visual span. The LMM-based framework of analysis, applied to the control of fixation durations in scenes, suggests important constraints for models of scene perception and search, and for visual attention in general

Experimental investigation of phase shifting in 1D Bragg structures for high power microwave pulse compression

The study of the quantum phase-space distribution of quarks and gluons inside nucleons in terms of TMDs and GPDs has become, in the last decade, a cutting-edge research field in hadron physics. These non-perturbative objects, respectively measurable in semi-inclusive deep-inelastic scattering and exclusive processes, allow to obtain 3-dimensional representations of the nucleon in the momentum and spatial coordinates as well as indirect insights into the still unknown parton orbital angular momentum. The HERMES experiment at HERA has been a precursor in this field. A selection of HERMES results sensitive to both TMDs and GPDs is presented

Modelling of free-electron maser based on two-dimensional distributed feedback

The use of two-dimensional (2D) distributed feedback has been considered as a method of providing spatially coherent radiation from an oversized annular electron beam used to drive a ITEM based on a coaxial two-mirror cavity. The operation of the FEM when the interaction space is formed by a 2D Bragg input and a 1D Bragg output mirror separated by a regular section of the coaxial waveguide has been studied using the 3D Particle-in-Cell code MAGIC. The properties of the FEM are analyzed and discussed. The single mode operation of the FEM that uses a coaxial cavity is demonstrated and the design of a 2D Bragg FEM-oscillator based on a high-current accelerator is discussed

Study of one-dimensional Bragg structures with localized defect

The results of studies of one-dimensional Bragg structures (one-dimensional periodic lattice) with localized defects are presented. The defects considered are localized, step changes (shifts) of the lattice phase (corrugation). The influence of the defects on the periodic lattice band-gap parameters has been analyzed. The presence of the defect resulted in the appearance of a pass band, associated with the defect eigenmode, inside the lattice band gap and it was demonstrated that the position of the pass band depended strongly on the parameters of the defect as well as the field structure. The experimental and theoretical results obtained are compared and discussed. © 2007 American Institute of Physics

Transmission profiling of phase shifted 1D Bragg reflectors in standard and coaxial waveguide

Bragg reflector can be defined as a region which shows a periodic change in the wave impedance, leading to gaps in the transmission pass-band. We report the results of initial experimental and theoretical work into the control of the transmission profiles of 1D Bragg reflectors, realized through the introduction of a +/-pi phase shift defect in the 1D corrugation

2D and 1D Surface Photonic Band Gap structures for accelerator applications

First measurements of microwave radiation from a coaxial Free-Electron Maser (FEM), based on a two-mirror cavity, formed by 2D and 1D Surface Photonic Band Gap (SPBG) structures (input and output mirrors) with an intermediate coaxial waveguide are presented. The input mirror provides two-dimensional distributed feedback and ensures mode selection over the wave azimuthal index. The use of a 1D Bragg structure as an output mirror reduces the cavity Q-factor, improves the RF field profiles inside the cavity and increases the output power compared to FEMs based solely on 2D SPBG structures. The FEM has been driven by an oversized, high-current (1.4kA), thin annular electron beam of 200ns pulse duration. An output power of ∼60MW corresponding to an efficiency of ~10% was measured. The directional mode pattern of the microwave radiation launched from the output horn was also measured. Using cut-off filters the location of the operating frequency was found to lie between 35 GHz and 39 GHz. The generation of high power microwave pulses in the Ka-band can be adapted to test the breakdown strength of advanced accelerator structures such as CLIC. The possibility to "condition" and to compress the pulse using active 1D SPBG structures is presented. The results of preliminary experiments show that the band gap location can be manipulated by adjustment of the phase between the periodic perturbations of an active 1D SPBG mirror