Validation of the performance of a GMO multiplex screening assay based on microarray detection

A new screening method for the detection and identification of GMO, based on the use of multiplex PCR followed by microarray, has been developed and is presented. The technology is based on the identification of quite ubiquitous GMO genetic target elements first amplified by PCR, followed by direct hybridisation of the amplicons on a predefined microarray (DualChip® GMO, Eppendorf, Germany). The validation was performed within the framework of a European project (Co-Extra, contract no 007158) and in collaboration with 12 laboratories specialised in GMO detection. The present study reports the strategy and the results of an ISO complying validation of the method carried out through an inter-laboratory study. Sets of blind samples were provided consisting of DNA reference materials covering all the elements detectable by specific probes present on the array. The GMO concentrations varied from 1% down to 0.045%. In addition, a mixture of two GMO events (0.1% RRS diluted in 100% TOPAS19/2) was incorporated in the study to test the robustness of the assay in extreme conditions. Data were processed according to ISO 5725 standard. The method was evaluated with predefined performance criteria with respect to the EC CRL method acceptance criteria. The overall method performance met the acceptance criteria; in particular, the results showed that the method is suitable for the detection of the different target elements at 0.1% concentration of GMO with a 95% accuracy rate. This collaborative trial showed that the method can be considered as fit for the purpose of screening with respect to its intra- and inter-laboratory accuracy. The results demonstrated the validity of combining multiplex PCR with array detection as provided by the DualChip® GMO (Eppendorf, Germany) for the screening of GMO. The results showed that the technology is robust, practical and suitable as a screening too

From Finite to Infinite Range Order via Annealing: The Causal Architecture of Deformation Faulting in Annealed Close-Packed Crystals

We analyze solid-state phase transformations that occur in zinc-sulfide crystals during annealing using a random deformation-faulting mechanism with a very simple interaction between adjacent close-packed double layers. We show that, through annealing, infinite-range structures emerge from initially short-range crystal order. That is, widely separated layers carry structurally significant information and so layer stacking cannot be completely described by any finite-range Markov process. We compare our results to two experimental diffraction spectra, finding excellent agreement.Comment: 7 pages, 6 figures; See http://www.santafe.edu/projects/CompMech/papers/iro.htm

A progressive refinement approach for the visualisation of implicit surfaces

Visualising implicit surfaces with the ray casting method is a slow procedure. The design cycle of a new implicit surface is, therefore, fraught with long latency times as a user must wait for the surface to be rendered before being able to decide what changes should be introduced in the next iteration. In this paper, we present an attempt at reducing the design cycle of an implicit surface modeler by introducing a progressive refinement rendering approach to the visualisation of implicit surfaces. This progressive refinement renderer provides a quick previewing facility. It first displays a low quality estimate of what the final rendering is going to be and, as the computation progresses, increases the quality of this estimate at a steady rate. The progressive refinement algorithm is based on the adaptive subdivision of the viewing frustrum into smaller cells. An estimate for the variation of the implicit function inside each cell is obtained with an affine arithmetic range estimation technique. Overall, we show that our progressive refinement approach not only provides the user with visual feedback as the rendering advances but is also capable of completing the image faster than a conventional implicit surface rendering algorithm based on ray casting

Competition and coexistence of bond and charge orders in (TMTTF)2AsF6

(TMTTF)2AsF6 undergoes two phase transitions upon cooling from 300 K. At Tco=103 K a charge-ordering (CO) occurs, and at Tsp(B=9 T)=11 K the material undergoes a spin-Peierls (SP) transition. Within the intermediate, CO phase, the charge disproportionation ratio is found to be at least 3:1 from carbon-13 NMR 1/T1 measurements on spin-labeled samples. Above Tsp, up to about 3Tsp, 1/T1 is independent of temperature, indicative of low-dimensional magnetic correlations. With the application of about 0.15 GPa pressure, Tsp increases substantially, while Tco is rapidly suppressed, demonstrating that the two orders are competing. The experiments are compared to results obtained from calculations on the 1D extended Peierls-Hubbard model.Comment: 4 pages, 5 figure

Ab-initio calculation of the 6Li{}^6Li binding energy with the Hybrid Multideterminant scheme

We perform an ab-initio calculation for the binding energy of ${}^6Li$ using the CD-Bonn 2000 NN potential renormalized with the Lee-Suzuki method. The many-body approach to the problem is the Hybrid Multideterminant method. The results indicate a binding energy of about $31 MeV$, within a few hundreds KeV uncertainty. The center of mass diagnostics are also discussed.Comment: 18 pages with 3 figures. More calculations added, to be published in EPJ

Insulator-Superfluid transition of spin-1 bosons in an optical lattice in magnetic field

We study the insulator-superfluid transition of spin-1 bosons in an optical lattice in a uniform magnetic field. Based on a mean-field approximation we obtained a zero-temperature phase diagram. We found that depending on the particle number the transition for bosons with antiferromagnetic interaction may occur into different superfluid phases with spins aligned along or opposite to the field direction. This is qualitatively different from the field-free transition for which the mean-field theory predicts a unique (polar) superfluid state for any particle number.Comment: 10 pages, 2 eps figure

Electronic and Structural Properties of a 4d-Perovskite: Cubic Phase of SrZrO3_3

First-principles density functional calculations are performed within the local density approximation to study the electronic properties of SrZrO$_3$, an insulating 4d-perovskite, in its high-temperature cubic phase, above 1400 K, as well as the generic 3d-perovskite SrTiO$_3$, which is also a d^0-insulator and cubic above 105 K, for comparison reasons. The energy bands, density of states and charge density distributions are obtained and a detailed comparison between their band structures is presented. The results are discussed also in terms of the existing data in the literature for both oxides.Comment: 5 pages, 2 figure

Theory of nuclear induced spectral diffusion: Spin decoherence of phosphorus donors in Si and GaAs quantum dots

We propose a model for spectral diffusion of localized spins in semiconductors due to the dipolar fluctuations of lattice nuclear spins. Each nuclear spin flip-flop is assumed to be independent, the rate for this process being calculated by a method of moments. Our calculated spin decoherence time $T_{M}=0.64$ ms for donor electron spins in Si:P is a factor of two longer than spin echo decay measurements. For $^{31}$P nuclear spins we show that spectral diffusion is well into the motional narrowing regime. The calculation for GaAs quantum dots gives $T_{M}=10-50$ $\mu$s depending on the quantum dot size. Our theory indicates that nuclear induced spectral diffusion should not be a serious problem in developing spin-based semiconductor quantum computer architectures.Comment: 15 pages, 9 figures. Accepted for publication in Phys. Rev.

Electron spin as a spectrometer of nuclear spin noise and other fluctuations

This chapter describes the relationship between low frequency noise and coherence decay of localized spins in semiconductors. Section 2 establishes a direct relationship between an arbitrary noise spectral function and spin coherence as measured by a number of pulse spin resonance sequences. Section 3 describes the electron-nuclear spin Hamiltonian, including isotropic and anisotropic hyperfine interactions, inter-nuclear dipolar interactions, and the effective Hamiltonian for nuclear-nuclear coupling mediated by the electron spin hyperfine interaction. Section 4 describes a microscopic calculation of the nuclear spin noise spectrum arising due to nuclear spin dipolar flip-flops with quasiparticle broadening included. Section 5 compares our explicit numerical results to electron spin echo decay experiments for phosphorus doped silicon in natural and nuclear spin enriched samples.Comment: Book chapter in "Electron spin resonance and related phenomena in low dimensional structures", edited by Marco Fanciulli. To be published by Springer-Verlag in the TAP series. 35 pages, 9 figure

Dual action antifungal small molecule modulates multidrug efflux and TOR signaling.

There is an urgent need for new strategies to treat invasive fungal infections, which are a leading cause of human mortality. Here, we establish two activities of the natural product beauvericin, which potentiates the activity of the most widely deployed class of antifungal against the leading human fungal pathogens, blocks the emergence of drug resistance, and renders antifungal-resistant pathogens responsive to treatment in mammalian infection models. Harnessing genome sequencing of beauvericin-resistant mutants, affinity purification of a biotinylated beauvericin analog, and biochemical and genetic assays reveals that beauvericin blocks multidrug efflux and inhibits the global regulator TORC1 kinase, thereby activating the protein kinase CK2 and inhibiting the molecular chaperone Hsp90. Substitutions in the multidrug transporter Pdr5 that enable beauvericin efflux impair antifungal efflux, thereby impeding resistance to the drug combination. Thus, dual targeting of multidrug efflux and TOR signaling provides a powerful, broadly effective therapeutic strategy for treating fungal infectious disease that evades resistance