Functional domains and the antiviral effect of the double-stranded RNA-dependent protein kinase PKR from Paralichthys olivaceus

The double-stranded RNA (dsRNA)-dependent protein kinase PKR is thought to mediate a conserved antiviral pathway by inhibiting viral protein synthesis via the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2 alpha). However, little is known about the data related to the lower vertebrates, including fish. Recently, the identification of PKR-like, or PKZ, has addressed the question of whether there is an orthologous PKR in fish. Here, we identify the first fish PKR gene from the Japanese flounder Paralichthys olivaceus (PoPKR). PoPKR encodes a protein that shows a conserved structure that is characteristic of mammalian PKRs, having both the N-terminal region for dsRNA binding and the C-terminal region for the inhibition of protein translation. The catalytic activity of PoPKR is further evidence that it is required for protein translation inhibition in vitro. PoPKR is constitutively transcribed at low levels and is highly induced after virus infection. Strikingly, PoPKR overexpression increases eIF2 alpha phosphorylation and inhibits the replication of Scophthalmus maximus rhabdovirus (SMRV) in flounder embryonic cells, whereas phosphorylation and antiviral effects are impaired in transfected cells expressing the catalytically inactive PKR-K421R variant, indicating that PoPKR inhibits virus replication by phosphorylating substrate eIF2 alpha. The interaction between PoPKR and eIF2 alpha is demonstrated by coimmunoprecipitation assays, and the transfection of PoPKR-specific short interfering RNA further reveals that the enhanced eIF2 alpha phosphorylation is catalyzed by PoPKR during SMRV infection. The current data provide significant evidence for the existence of a PKR-mediated antiviral pathway in fish and reveal considerable conservation in the functional domains and the antiviral effect of PKR proteins between fish and mammals.

Solar UV radiation drives CO2 fixation in marine phytoplankton: A double-edged sword

Photosynthesis by phytoplankton cells in aquatic environments contributes to more than 40% of the global primary production (Behrenfeld et al., 2006). Within the euphotic zone (down to 1% of surface photosynthetically active radiation [PAR]), cells are exposed not only to PAR (400-700 nm) but also to UV radiation (UVR; 280-400 nm) that can penetrate to considerable depths (Hargreaves, 2003). In contrast to PAR, which is energizing to photosynthesis, UVR is usually regarded as a stressor (Hader, 2003) and suggested to affect CO2-concentrating mechanisms in phytoplankton (Beardall et al., 2002). Solar UVR is known to reduce photosynthetic rates (Steemann Nielsen, 1964; Helbling et al., 2003), and damage cellular components such as D1 proteins (Sass et al., 1997) and DNA molecules (Buma et al., 2003). It can also decrease the growth (Villafane et al., 2003) and alter the rate of nutrient uptake (Fauchot et al., 2000) and the fatty acid composition (Goes et al., 1994) of phytoplankton. Recently, it has been found that natural levels of UVR can alter the morphology of the cyanobacterium Arthrospira (Spirulina) platensis (Wu et al., 2005b). On the other hand, positive effects of UVR, especially of UV- A (315-400 nm), have also been reported. UV- A enhances carbon fixation of phytoplankton under reduced (Nilawati et al., 1997; Barbieri et al., 2002) or fast-fluctuating (Helbling et al., 2003) solar irradiance and allows photorepair of UV- B-induced DNA damage (Buma et al., 2003). Furthermore, the presence of UV-A resulted in higher biomass production of A. platensis as compared to that under PAR alone (Wu et al., 2005a). Energy of UVR absorbed by the diatom Pseudo-nitzschia multiseries was found to cause fluorescence (Orellana et al., 2004). In addition, fluorescent pigments in corals and their algal symbiont are known to absorb UVR and play positive roles for the symbiotic photosynthesis and photoprotection (Schlichter et al., 1986; Salih et al., 2000). However, despite the positive effects that solar UVR may have on aquatic photosynthetic organisms, there is no direct evidence to what extent and howUVR per se is utilized by phytoplankton. In addition, estimations of aquatic biological production have been carried out in incubations considering only PAR (i. e. using UV-opaque vials made of glass or polycarbonate; Donk et al., 2001) without UVR being considered (Hein and Sand-Jensen, 1997; Schippers and Lurling, 2004). Here, we have found that UVR can act as an additional source of energy for photosynthesis in tropical marine phytoplankton, though it occasionally causes photoinhibition at high PAR levels. While UVR is usually thought of as damaging, our results indicate that UVR can enhance primary production of phytoplankton. Therefore, oceanic carbon fixation estimates may be underestimated by a large percentage if UVR is not taken into account.

Integration of double-fluorescence expression vectors into zebrafish genome for the selection of site-directed knockout/knockin

Production of zebrafish by modifying endogenous growth hormone (GH) gene through homologous recombination is described here. We first constructed the targeting vectors pGHT1.7k and pGHT2.8k, which were used for the knockout/knockin of the endogenous GH gene of zebrafish, and injected these two vectors into the embryos of zebrafish. Overall, the rate of targeted integration with the characteristic of germ line transmission in zebrafish was 1.7x10(-6). In one experimental patch, the integrating efficiency of pGHT2.8k was higher than that of pGHT1.7k, but the lethal effect of pGHT2.8k was stronger than that of pGHT1.7k. The clones with the correct integration of target genes were identified by a simple screening procedure based on green fluorescent protein (GFP) and RFP dual selection, which corresponded to homologous recombination and random insertion, respectively. The potential homologous recombination zebrafish was further bred to produce a heterozygous F-1 generation, selected based on the presence of GFP. The potential targeted integration of exogenous GH genes into a zebrafish genome at the P-0 generation was further verified by polymerase chain reaction and Southern blot analysis. Approximately 2.5% of potential founder knockout and knockin zebrafish had the characteristic of germ line transmission. In this study, we developed an efficient method for producing the targeted gene modification in zebrafish for future studies on genetic modifications and gene functions using this model organism.

Origin of the double- and multi-pulse structure of echolocation signals in Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientialis)

The signals of dolphins and porpoises often exhibit a multi-pulse structure. Here, echolocation signal recordings were made from four geometrically distinct positions of seven Yangtze finless porpoises temporarily housed in a relatively small, enclosed area. Some clicks demonstrated double-pulse, and others multi-pulse, structure. The interpulse intervals between the first and second pulse of the double- and multi-pulse clicks were significantly different among data from the four different positions (p < 0.01, one-way ANOVA). These results indicate that the interpulse interval and structure of the double- and multi-pulse echolocation signals depend on the hydrophone geometry of the animal, and that the double- and multi-pulse structure of echolocation signals in Yangtze finless porpoise is not caused by the phonating porpoise itself, but by the multipath propagation of the signal. Time delays in the 180 degrees phase-shifted surface reflection pulse and the nonphase-shifted bottom reflection pulse of the multi-pulse structures, relative to the direct signal, can be used to calculate the distance to a phonating animal. (c) 2005 Acoustical Society of America.

Interference in transport through double barriers in interacting quantum wires

We investigate interference effects of the backscattering current through a double-barrier structure in an interacting quantum wire attached to noninteracting leads. Depending on the interaction strength and the location of the barriers, the backscattering current exhibits different oscillation and scaling characteristics with the applied voltage in the strong and weak interaction cases. However, in both cases, the oscillation behaviors of the backscattering current are mainly determined by the quantum mechanical interference due to the existence of the double barriers.

Degree of fourth-order coherence by double Hanbury Brown-Twiss detections

Photon quantum statistics of light can be shown by the high-order coherence. The fourth-order coherences of various quantum states including Pock states, coherent states, thermal states and squeezed vacuum states are investigated based on a double Banbury Brown Twiss (HBT) scheme. The analytical results are obtained by taking the overall efficiency and background into account.

QtUCP-A program for determining unit-cell parameters in electron diffraction experiments using double-tilt and rotation-tilt holders

A computer program, QtUCP, has been developed based on several well-established algorithms using GCC 4.0 and Qt (R) 4.0 (Open Source Edition) under Debian GNU/Linux 4.0r0. it can determine the unit-cell parameters from an electron diffraction tilt series obtained from both double-tilt and rotation-tilt holders. In this approach, two or more primitive cells of the reciprocal lattice are determined from experimental data, in the meantime, the measurement errors of the tilt angles are checked and minimized. Subsequently, the derived primitive cells are converted into the reduced form and then transformed into the reduced direct primitive cell. Finally all the patterns are indexed and the least-squares refinement is employed to obtain the optimized results of the lattice parameters. Finally, two examples are given to show the application of the program, one is based on the experiment, the other is from the simulation. (C) 2008 Elsevier B.V. All rights reserved.

Transmission properties through a double quantum dot with a wave packet

The transmiss on time and tunneling probability of an electron through a double quantum dot are studied using the transfer matrix technique. The time-dependent Schrodinger equation is applied for a Gaussian wave packet passing through the double quantum clot. The numerical calculations are carried out for a double quantum clot consisting of GaAs/InAs material. We find that the electron tunneling resonance peaks split when the electron transmits through the double quantum dot. The splitting energy increases as the distance between the two quantum dots decreases. The transmission time can be elicited from the temporal evolution of the Gaussian wave packet in the double quantum dot. The transmission time increases quickly as the thickness of tire barrier increases. The lifetime of the resonance state is calculated tram the temporal evolution of the Gaussian-state at the centers of quantum dots.

Resonant tunneling through double-bended graphene nanoribbons

We investigate theoretically resonant tunneling through double-bended graphene nanoribbon (GNR) structures, i.e., armchair-edged GNRs (AGNRs) in between two semi-infinite zigzag GNR leads. Our numerical results demonstrate that the resonant tunneling can be tuned dramatically by the Fermi energy and the length and/or widths of the AGNR for both the metallic and semiconductorlike AGNRs. The structure can also be use to control the valley polarization of the tunneling currents and could be useful for potential application in valleytronics devices. (C) 2008 American Institute of Physics.

Confined LO-phonon-assisted magnetotunneling in a parabolic quantum well with double barriers

The confined longitudinal-optical phonon-assisted tunneling through a parabolic quantum well with double barriers in a magnetic field perpendicular to the interfaces is studied theoretically based on a dielectric continuum model. The numerical results show that the applied magnetic field sharpens and heightens the phonon-assisted tunneling peaks in agreement with experimental observation. Furthermore, the phonon-assisted magnetotunneling peaks shift towards the higher biases as the magnetic field increases. In contrast to the results for a rectangular quantum well, the ratio of peak to valley of the phonon-assisted tunneling is larger for the wider well case. It also indicates that the phonon-assisted tunneling current peaks can be easily observed for a wider parabolic quantum well. (C) 2008 Published by Elsevier B.V.

Fiber laser hydrophone based on double diaphragms: Theory and experiment

A fiber laser hydrophone with enhanced sensitivity is demonstrated. Two diaphragms with a hard core fixed at each center are used as the sensing element. Theoretical analysis shows that the Young's modulus of the diaphragm and the radius of the hard core have significant effect on the acoustic sensitivity. Experiments are carried out to test this effect and the performance of the hydrophone. The experimental result agrees well with the theoretical result, and a sensitivity of 7 nm/MPa has been achieved.

Coulomb blockade double-dot Aharonov-Bohm interferometer: Giant fluctuations

Electron transport through two parallel quantum dots is a kind of solid-state realization of double path interference We demonstrate that the inter-clot Coulomb correlation and quantum coherence would result in strong current fluctuations with a divergent Fano factor at zero frequency. We also provide physical interpretation for this surprising result, which displays its generic feature and allows us to recover this phenomenon in more complicated systems. (C) 2009 Elsevier B.V. All rights reserved.

Coulomb blockade double-dot Aharonov-Bohm interferometer: Harmonic decomposition of the interference pattern

For the solid-state double-dot interferometer, the phase shifted interference pattern induced by the interplay of inter-dot Coulomb correlation and multiple reflections is analyzed by harmonic decomposition. Unexpected result is uncovered, and is discussed in connection with the which-path detection and electron loss. (C) 2009 Elsevier B.V. All rights reserved.

FBG pressure sensor based on the double shell cylinder with temperature compensation

A novel fiber Bragg grating (FBG) pressure sensor based on the double shell cylinder with temperature compensation is presented. in the sensing scheme, a sensing FBG is affixed in the tangential direction on the outer surface of the inner cylinder, and another FBG is affixed in the axial direction to compensate the temperature fluctuation. Based on the theory of elasticity, the theoretical analysis of the strain distribution of the sensing shell is presented. Experiments are carried out to test the performance of the sensor. A pressure sensitivity of 0.0937 nm/MPa has been achieved. The experimental results also demonstrate that the two FBGs have the same temperature sensitivity, which can be utilized to compensate the temperature induced wavelength shift during the pressure measurement. (C) 2008 Elsevier Ltd. All rights reserved.

Properties of AlyGa1-yN/AlxGa1-xN/AlN/GaN Double-Barrier High Electron Mobility Transistor Structure

Electrical properties of AlyGa1-yN/AlxGa1-xN/AlN/GaN structure are investigated by solving coupled Schrodinger and Poisson equation self-consistently. Our calculations show that the two-dimensional electron gas (2DEG) density will decrease with the thickness of the second barrier (AlyGa1-yN) once the AlN content of the second barrier is smaller than a critical value y(c), and will increase with the thickness of the second barrier (AlyGa1-yN) when the critical AlN content of the second barrier y(c) is exceeded. Our calculations also show that the critical AlN content of the second barrier y(c) will increase with the AlN content and the thickness of the first barrier layer (AlxGa1-xN).