Adaptive evolution of primate TRIM5 alpha, a gene restricting HIV-1 infection

Recent studies showed that nonhuman primate TRIM5 alpha can efficiently block HIV-1 infection in human cell lines. It can also restrict other retroviruses, therefore, suggested as a general defender against retrovirus infection. Here, we present an evolutionary analysis of TRIM5 alpha in primates. Our results demonstrated that TRIM5a has been evolving rapidly in primates, which is likely caused by Darwinian positive selection. The SPRY domain of TRM5 alpha, which may be responsible for recognition of incoming viral capsids showed higher nonsynonymous/synonymous substitution ratios than the non-SPRY domain, indicating that the adaptive evolution of TRIM5a ill primates might be an innate strategy developed in defending retrovirus infection during primate evolution. In addition, the comparative protein sequence analysis suggested that the amino acid substitution pattern at a single site (344R/Q/P) located in the SPRY domain may explain the differences in Susceptibilities of HIV-1 infection in diverse primate species. (c) 2005 Elsevier B.V. All rights reserved.

Seasonal variations in stable isotope ratios of two biomanipulation fishes and seston in a large pen culture in hypereutrophic Meiliang Bay, Lake Taihu

This paper reports on seasonal changes in stable carbon and nitrogen isotope ratios of seston and muscle tissue of silver carp and bighead carp during 2004 and 2005, focusing primarily on the carbon sources and trophic relationships among phytoplankton, zooplankton and silver carp and bighead carp in a large fish pen of Meiliang Bay (Lake Taihu, China). delta C-13 showed a minimal value in March 2005 and a maximal value in August 2005 in seston both inside and outside the pen, whereas delta N-15 of seston showed the minimum in winter and the maximum during algal blooms. A positive correlation between delta C-13 of silver carp and that of seston suggested that temporal variation Of delta C-13 in seston was preserved in fish via the food chain. The differences of delta C-13 among seston, zooplankton and muscle tissue of silver carp and bighead carp ranged only 0.2-1.7%, indicating that plankton production was the primary food source of filter-feeding fishes. According to a mass balance model, we estimated that the contributions of zooplankton to the diets of silver carp and bighead carp were 45.7% and 54.3%, respectively, based on the delta N-15 values of zooplankton and planktivorous fishes. (C) 2007 Elsevier B.V. All rights reserved

Studies on the food web structure of Lake Donghu using stable carbon and nitrogen isotope ratios

Food web structure was studied by using carbon and nitrogen isotope ratios in a hypereutrophic subtropical Chinese lake, Lake Donghu. High external nutrient loading and the presence of abundant detritus from submersed macrophytes were responsible for the high sediment delta(15)N and delta(13)C, respectively. C-13 was significantly higher in submersed macrophytes than in other macrophytes. The similar delta(13)C values in phytoplankton, zooplankton, zoobenthos, and planktivorous fish indicate that phytoplankton was the major food source for the consumers. By using a delta(15)N mass balance model, we estimate that the contributions of zooplankton to the diet of silver carp and bighead carp were 54% and 74%, respectively, which is in agreement with previous microscopic observations on intestinal contents of these fishes.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

Distribution, transformation, and long-term accumulation of polychlorinated dibenzo-p-dioxins and dibenzofurans in different tissues of fish and piscivorous birds

The present study monitored 10-year-old fish and piscivorous birds from sites contaminated for many Stars. The data reflected the results of actual, long-term environmental exposures, The results demonstrate that different tissues of fish have quite different concentrations of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F), The concentration order of PCDD/F within fish is liver congruent to egg congruent to intestines kidney congruent to hearts gill congruent to bladders > muscle > brain. The concentration order of PCDD/F within piscivorous birds was livers egg congruent to hearts muscle congruent to stomachs brain, The results obtained also demonstrate that the accumulation patterns of piscivorous birds and fish are quite different. The tissues of fish and piscivorous birds have different capacities for bioaccumulation and biotransformation of PCDD/F; variable proportions of TEQs were also found throughout their bodies. In fish, toxic equivalency quotient (TEQ): PCDD/F ratios in various tissues ranged from 0.01 to 0.07, whereas in birds the ratios ranged from 0.07 to 0.43. If the concentrations are normalized with lipid content, the results vary less. The effect of different lipid properties is obvious in the case of brain tissue, which is richer in phospholipids. (C) 2000 Academic Press.

High repetition rate Q-switched microchip Nd:YVO4 laser with pulse duration as short as 1.1 ns

We have demonstrated a compact and an efficient passively Q-switched microchip Nd:YVO4 laser by using a composite semiconductor absorber as well as an output coupler. The composite semiconductor absorber was composed of an LT (low-temperature grown) In0.25Ga0.75As absorber and a pure GaAs absorber. To our knowledge, it was the first demonstration of the special absorber for Q-switching operation of microchip lasers. Laser pulses with durations of 1.1 ns were generated with a 350 mu m thick laser crystal and the repetition rate of the pulses was as high as 4.6 MHz. The average output power was 120 mW at the pump power of 700 mW. Pulse duration can be varied from 1.1 to 15.7 ns by changing the cavity length from 0.45 to 5 mm. Pulses with duration of 1.67 and 2.41 ns were also obtained with a 0.7 mm, thick laser crystal and a 1 mm thick laser crystal, respectively. (C) 2007 Elsevier GmbH. All rights reserved.

Comparison of Q-factors between TE and TM modes in 3-D microsquares by FDTD simulation

Mode characteristics of three-dimensional (3-D) microsquare resonators are investigated by finite-difference time-domain (FDTD) simulation for the transverse electric (TE)-like and the transverse magnetic (TM)-like modes. For a pillar microsquare with a side length of 2 pin in air, we have Q-factors about 5 X. 103 for TM-like modes at the wavelength of 1550 run, which are one order larger than those of TE-like modes, as vertical refractive index distribution is 3.17/3.4/3.17 and the cororresponding center layer thickness is 0.2 mu m. The mode field patterns show that TM-like modes have much weaker vertical radiation coupling loss than TE-like modes. TM-like modes can have high Q-factors in a microsquare with weak vertical field confinement.

Design of quantum cascade microcavity lasers based on Q factor versus etching depth

The choice of the etching depth for semiconductor microcavities is a compromise between a high Q factor and a difficult technique in a practical fabricating process. In this paper, the influences of the etching depth on mode Q factors for mid-infrared quantum cascade microcylinder and microsquare lasers around 4.8 and 7.8 mu m are simulated by three-dimensional (3D) finite-difference time-domain (FDTD) techniques. For the microcylinder and the microsquare resonators, the mode Q factors of the whispering-gallery modes (WGMs) increase exponentially and linearly with the increase in the etching depth, respectively Furthermore, the mode Q factors of some higher order transverse WGMs may be larger than that of the fundamental transverse WGM in 3D microsquares. Based on the field distribution of the vertical multilayer slab waveguide and the mode Q factors versus the etching depth, the necessary etching depth is chosen at the position where the field amplitude is 1% of the peak value of the slab waveguide. In addition, the influences of sidewall roughness on the mode Q factors are simulated for microsquare resonators by 2D FDTD simulation. (C) 2009 Optical Society of America

High efficiency passively Q-switched mode-locking Nd:GdVO4 laser with LT-In0.25Ga0.75As saturable absorber

The generation of passively Q-switched mode-locking operation with 100% modulation depth has been observed from a diode-pumped Nd GdVO4 laser with a low temperature In0.25Ga0.75As saturable absorber, which was grown by the metal-organic chemical-vapor deposition technique and acted as saturable absorber as well as output coupler. The repetition rate and pulse duration of the mode-locked pulses concentrated in the Q-switch envelop were 455 MHz and 12 ps, respectively. The average output power was 1.8 W and the slope efficiency was 36%. (C) 2009 Elsevier B.V. All rights reserved.

Passive Q-switched mode locking of double-clading Yb : fiber laser with ion-implanted GaAs

We report the technique of the ion-implanted semi-insulating GaAs wafer used for passive Q-switched mode locking in double-cladding Yb:fiber laser. The wafer was implanted with 400-keV energy, 10(16)/cm(2) dose As+ ions, and was annealed at 600degreesC for 20 min. At the pump power of 5W, we achieved output power of 200mW. The repetition rate of envelope of Q-switched mode locking is 50-kHz with a FWHM envelope of 4mus. The repetition rate of mode locked pulse train was found to be 15-MHz. This is the first report of such a kind of laser to the best of our knowledge.

Antiphase state in passively Q-switched Yb : YAG microchip multimode lasers with a saturable absorber GaAs

We report on recent experimental results of the spontaneous antiphase dynamics that occurs in a laser-diode-pumped multimode passively Q-switched microchip Yb:YAG (where YAG is yttrium aluminum garnet) lasers with a saturable absorber GaAs. We observe that the pulse sequence of the first mode characterized by one, two, and three pulses as a group and all the modes display an antiphase state as the pumping ratio rises. We modify the multimode rate equations to account for nonlinear absorption due to GaAs in the presence of spatial hole burning. We perform numerical simulations based on the proposed rate equations and reproduce the observed antiphase state of two and three active modes.

Observation of antiphase states in a passively Q-switched multimode microchip Yb : YAG laser with a GaAs saturable absorber

Antiphase dynamics has been observed experimentally for the laser modes operation in a laser-diode-pumped Q-switched microchip Yb:YAG laser with GaAs as a saturable absorber in the presence of spatial hole-burning. The Q-switched pulses sequences of two modes at different pump power have been obtained. The experimental results have shown that the pulses sequences displayed classic antiphase dynamics. (C) 2003 Elsevier B.V. All rights reserved.