DIGAP - a Database of Improved Gene Annotation for Phytopathogens

<p>Abstract</p> <p>Background</p> <p>Bacterial plant pathogens are very harmful to their host plants, which can cause devastating agricultural losses in the world. With the development of microbial genome sequencing, many strains of phytopathogens have been sequenced. However, some misannotations exist in these phytopathogen genomes. Our objective is to improve these annotations and store them in a central database DIGAP.</p> <p>Description</p> <p>DIGAP includes the following improved information on phytopathogen genomes. (i) All the 'hypothetical proteins' were checked, and non-coding ORFs recognized by the Z curve method were removed. (ii) The translation initiation sites (TISs) of 20% ~ 25% of all the protein-coding genes have been corrected based on the NCBI RefSeq, ProTISA database and an <it>ab initio </it>program, GS-Finder. (iii) Potential functions of about 10% 'hypothetical proteins' have been predicted using sequence alignment tools. (iv) Two theoretical gene expression indices, the codon adaptation index (CAI) and the <it>E</it>(<it>g</it>) index, were calculated to predict the gene expression levels. (v) Potential agricultural bactericide targets and their homology-modeled 3D structures are provided in the database, which is of significance for agricultural antibiotic discovery.</p> <p>Conclusion</p> <p>The results in DIGAP provide useful information for understanding the pathogenetic mechanisms of phytopathogens and for finding agricultural bactericides. DIGAP is freely available at <url>http://ibi.hzau.edu.cn/digap/</url>.</p

Promoting H2O2 production via 2-electron oxygen reduction by coordinating partially oxidized Pd with defect carbon.

Electrochemical synthesis of H2O2 through a selective two-electron (2e-) oxygen reduction reaction (ORR) is an attractive alternative to the industrial anthraquinone oxidation method, as it allows decentralized H2O2 production. Herein, we report that the synergistic interaction between partially oxidized palladium (Pdδ+) and oxygen-functionalized carbon can promote 2e- ORR in acidic electrolytes. An electrocatalyst synthesized by solution deposition of amorphous Pdδ+ clusters (Pd3δ+ and Pd4δ+) onto mildly oxidized carbon nanotubes (Pdδ+-OCNT) shows nearly 100% selectivity toward H2O2 and a positive shift of ORR onset potential by ~320 mV compared with the OCNT substrate. A high mass activity (1.946 A mg-1 at 0.45 V) of Pdδ+-OCNT is achieved. Extended X-ray absorption fine structure characterization and density functional theory calculations suggest that the interaction between Pd clusters and the nearby oxygen-containing functional groups is key for the high selectivity and activity for 2e- ORR

Parallel Computing of Polymer Chains Based on Monte Carlo Method

Computer simulation of polymer chain is carried out by Monte Carlo method in this paper. The properties of polymer chain are simulated by self avoiding walk and bond fluctuation model. The parallel computing model is established to solve the physical problems of the polymer chains. We analyze the algorithms for polymer chains to parallel computing at high performance computing center. Gustafson law is analyzed and is applied to obtain linear speedup

Design of Novel Reconfigurable Reflectarrays with Single-bit Phase Resolution for Ku-Band Satellite Antenna Applications

Reconfigurable reflectarray antennas operating in Ku-band are presented in this paper. First, a novel multilayer unit-cell based on polarization turning concept is proposed to achieve the single-bit phase shift required for reconfigurable reflectarray applications. The principle of the unit-cell is discussed using the current model and the space match condition, along with simulations to corroborate the design and performance criteria. Then, an offset-fed configuration is developed to verify performance of the unit-cell in antenna application, and its polarization transformation property is elaborated. Finally, an offset-fed reflectarray with 10×10 elements is developed and fabricated. The dual-polarized antenna utilizes the control code matrices to accomplish a wide angle beam-scanning. A full wave analysis is applied to the reflectarray, and detailed results are presented and discussed. This electronically steerable reflectarray antenna has significant potential for satellite applications, due to its wide operating band, simple control and beam-scanning capability

Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins

Type I IFNs are key cytokines mediating innate antiviral immunity. cGMP-AMP synthase, ritinoic acid-inducible protein 1 (RIG-I)–like receptors, and Toll-like receptors recognize microbial double-stranded (ds)DNA, dsRNA, and LPS to induce the expression of type I IFNs. These signaling pathways converge at the recruitment and activation of the transcription factor IRF-3 (IFN regulatory factor 3). The adaptor proteins STING (stimulator of IFN genes), MAVS (mitochondrial antiviral signaling), and TRIF (TIR domain-containing adaptor inducing IFN-β) mediate the recruitment of IRF-3 through a conserved pLxIS motif. Here we show that the pLxIS motif of phosphorylated STING, MAVS, and TRIF binds to IRF-3 in a similar manner, whereas residues upstream of the motif confer specificity. The structure of the IRF-3 phosphomimetic mutant S386/396E bound to the cAMP response element binding protein (CREB)-binding protein reveals that the pLxIS motif also mediates IRF-3 dimerization and activation. Moreover, rotavirus NSP1 (nonstructural protein 1) employs a pLxIS motif to target IRF-3 for degradation, but phosphorylation of NSP1 is not required for its activity. These results suggest a concerted mechanism for the recruitment and activation of IRF-3 that can be subverted by viral proteins to evade innate immune responses

Compact Metasurface Terahertz Spectrometer

The electromagnetic spectrum in the terahertz frequency region is of significant importance for understanding the formation and evolution of galaxies and stars throughout the history of the universe and the process of planet formation. Within the star forming clouds the constituent atoms and molecules are excited to produce characteristic emission and absorption lines, many of which happen at the terahertz frequencies. Thus, detecting the spectral signatures as unique fingerprints of molecules and atoms require terahertz spectrometers, which need to be operated in a space observatory because of the water vapor absorption in the earth atmosphere. However, current terahertz spectrometers face several challenges that limit their performances and applications, including a low resolution, limited bandwidth, large volume, and complexity. In this paper, we address the last two issues by demonstrating a concept of a compact terahertz spectrometer using metasurface. We start by modelling, designing, and fabricating a metasurface, aiming to optimize its performance within a band from 1.7 to 2.5 THz. Next, we make use of an array of quantum cascade lasers that operate at slightly different frequencies around 2.1 THz to validate the performance of the spectrometer. Finally, we apply the spectrum inversion method to analyse the measured data to confirm a resolution R of at least 273. Our results demonstrated a miniaturized terahertz spectrometer concept successfully

Two-Photon Scattering by a Cavity-Coupled Two-Level Emitter in a One-Dimensional Waveguide

We show that two-photon transport can be modulated by a two-level emitter coupled to a cavity in a one-dimensional waveguide. In the ordinary case, the transmitted light has a wider frequency spectrum than the situation without the cavity because it is reflected and scattered many times. But when the two photons are resonant with the cavity resonance reflection frequency, the frequency spectrum of the transmitted light becomes narrower than that without the cavity. This means that properly tuning the cavity resonance frequency can improve the photon-photon interaction. In addition, we show that the two-photon intensity correlation functions are nearly opposite to each other at the two sides of the emitter transition frequency rather than be the same, which is exactly the Fano resonance line shape for two photons. Such an effect is important for lowering the power threshold in optical bistable devices and for sensing applications. When the emitter transition frequency equals to the cavity resonance frequency for a high-Q cavity, our results agree with the recent experiments and theories.Comment: 12 pages, 16 figure

Effects of Y incorporation in TaON gate dielectric on electrical performance of GaAs metal-oxide-semiconductor capacitor

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