Gated rotation mechanism of site-specific recombination by ϕC31 integrase

Integrases, such as that of the Streptomyces temperate bacteriophage ϕC31, promote site-specific recombination between DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA. ϕC31 integrase belongs to the serine recombinase family, a large group of structurally related enzymes with diverse biological functions. It has been proposed that serine integrases use a “subunit rotation” mechanism to exchange DNA strands after double-strand DNA cleavage at the two recombining att sites, and that many rounds of subunit rotation can occur before the strands are religated. We have analyzed the mechanism of ϕC31 integrase-mediated recombination in a topologically constrained experimental system using hybrid “phes” recombination sites, each of which comprises a ϕC31 att site positioned adjacent to a regulatory sequence recognized by Tn3 resolvase. The topologies of reaction products from circular substrates containing two phes sites support a right-handed subunit rotation mechanism for catalysis of both integrative and excisive recombination. Strand exchange usually terminates after a single round of 180° rotation. However, multiple processive “360° rotation” rounds of strand exchange can be observed, if the recombining sites have nonidentical base pairs at their centers. We propose that a regulatory “gating” mechanism normally blocks multiple rounds of strand exchange and triggers product release after a single round

Towards electron transport measurements in chemically modified graphene: The effect of a solvent

Chemical functionalization of graphene modifies the local electron density of the carbon atoms and hence electron transport. Measuring these changes allows for a closer understanding of the chemical interaction and the influence of functionalization on the graphene lattice. However, not only chemistry, in this case diazonium chemistry, has an effect on the electron transport. Latter is also influenced by defects and dopants resulting from different processing steps. Here, we show that solvents used in the chemical reaction process change the transport properties. In more detail, the investigated combination of isopropanol and heating treatment reduces the doping concentration and significantly increases the mobility of graphene. Furthermore, the isopropanol treatment alone increases the concentration of dopants and introduces an asymmetry between electron and hole transport which might be difficult to distinguish from the effect of functionalization. The results shown in this work demand a closer look on the influence of solvents used for chemical modification in order to understand their influence

Particle-in-cell simulations of collisionless magnetic reconnection with a non-uniform guide field

Results are presented of a first study of collisionless magnetic reconnection starting from a recently found exact nonlinear force-free Vlasov–Maxwell equilibrium. The initial state has a Harris sheet magnetic field profile in one direction and a non-uniform guide field in a second direction, resulting in a spatially constant magnetic field strength as well as a constant initial plasma density and plasma pressure. It is found that the reconnection process initially resembles guide field reconnection, but that a gradual transition to anti-parallel reconnection happens as the system evolves. The time evolution of a number of plasma parameters is investigated, and the results are compared with simulations starting from a Harris sheet equilibrium and a Harris sheet plus constant guide field equilibrium

Steam storage systems for flexible biomass CHP plants - Evaluation and initial model based calculation

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Within the present study a novel concept for the demand-oriented power generation of a solid-biomass fueled combined heat and power (CHP) plant is investigated. The integration of a steam storage system into the plants process enables a decoupling of the steam (boiler) and the power generation (steam turbine). By buffering the steam, the power output of the turbine can be adjusted without changing the rated thermal capacity of the plant. Various available storage systems are selected and comparatively evaluated applying the adapted analytic hierarchy process (AHP). The technology assessment revealed that the combination of a steam accumulator and solid concrete storage represents the best suiting option. An initial model based simulation study is performed to identify the fundamental behaviour of this system, integrated in a biomass CHP plant. The operation principle is has proved their technical feasibility and seems to be applicable at a commercial scale. According to the modelling results flexible short term power generation in a time range of up to fifteen minutes is applicable. A load-range of almost the plants rated capacity can be achieved

Nonlinear wavelength conversion in photonic crystal fibers with three zero dispersion points

In this theoretical study, we show that a simple endlessly single-mode photonic crystal fiber can be designed to yield, not just two, but three zero-dispersion wavelengths. The presence of a third dispersion zero creates a rich phase-matching topology, enabling enhanced control over the spectral locations of the four-wave-mixing and resonant-radiation bands emitted by solitons and short pulses. The greatly enhanced flexibility in the positioning of these bands has applications in wavelength conversion, supercontinuum generation and pair-photon sources for quantum optics

PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE

One-Bead Microrheology with Rotating Particles

We lay the theoretical basis for one-bead microrheology with rotating particles, i.e, a method where colloids are used to probe the mechanical properties of viscoelastic media. Based on a two-fluid model, we calculate the compliance and discuss it for two cases. We first assume that the elastic and fluid component exhibit both stick boundary conditions at the particle surface. Then, the compliance fulfills a generalized Stokes law with a complex shear modulus whose validity is only limited by inertial effects, in contrast to translational motion. Secondly, we find that the validity of the Stokes regime is reduced when the elastic network is not coupled to the particleComment: 7 pages, 5 figures, submitted to Europhys. Let

Strange nonchaotic attractors in noise driven systems

Strange nonchaotic attractors (SNAs) in noise driven systems are investigated. Before the transition to chaos, due to the effect of noise, a typical trajectory will wander between the periodic attractor and its nearby chaotic saddle in an intermittent way, forms a strange attractor gradually. The existence of SNAs is confirmed by simulation results of various critera both in map and continuous systems. Dimension transition is found and intermittent behavior is studied by peoperties of local Lyapunov exponent. The universality and generalization of this kind of SNAs are discussed and common features are concluded

Physical State of Molecular Gas in High Galactic Latitude Translucent Clouds

The rotational transitions of carbon monoxide (CO) are the primary means of investigating the density and velocity structure of the molecular interstellar medium. Here we study the lowest four rotational transitions of CO towards high-latitude translucent molecular clouds (HLCs). We report new observations of the J = (4-3), (2-1), and (1-0) transitions of CO towards eight high-latitude clouds. The new observations are combined with data from the literature to show that the emission from all observed CO transitions is linearly correlated. This implies that the excitation conditions which lead to emission in these transitions are uniform throughout the clouds. Observed 13CO/12CO (1-0) integrated intensity ratios are generally much greater than the expected abundance ratio of the two species, indicating that the regions which emit 12CO (1-0) radiation are optically thick. We develop a statistical method to compare the observed line ratios with models of CO excitation and radiative transfer. This enables us to determine the most likely portion of the physical parameter space which is compatible with the observations. The model enables us to rule out CO gas temperatures greater than 30K since the most likely high-temperature configurations are 1 pc-sized structures aligned along the line of sight. The most probable solution is a high density and low temperature (HDLT) solution. The CO cell size is approximately 0.01 pc (2000 AU). These cells are thus tiny fragments within the 100 times larger CO-emitting extent of a typical high-latitude cloud. We discuss the physical implications of HDLT cells, and we suggest ways to test for their existence.Comment: 19 pages, 13 figures, 2 tables, emulateapj To be published in The Astrophysical Journa