Comparison of mitochondrial genome and development of specific PCR primers for identifying two scuticociliates, Pseudocohnilembus persalinus and Uronema marinum.

BACKGROUND: Pseudocohnilembus persalinus and Uronema marinum (Ciliophora, Scuticociliatia), as parasitic scuticociliatid ciliates, were isolated from Scophthalmus maximus and Takifugu rubripes, respectively, in our previous studies. These ciliates are morphologically very similar; hence, it is difficult to identify specific scuticociliate species using traditional classification methods for performing taxonomic research and disease control studies. METHODS: We annotated the mitochondrial genomes of these two scuticociliates on the basis of previous sequencing, including analyses of nucleotide composition, codon usage, Ka/Ks, and p-distance. We also compared the nucleotide and amino acid similarity of the mitochondrial genomes of P. persalinus, U. marinum, and other 12 related ciliates, and a phylogenetic tree was constructed using 16 common genes. We chose the nad4 and nad7 genes to design specific PCR primers for identification. RESULTS: P. persalinus and U. marinum were found to have a close evolutionary relationship. Although codon preferences were similar, differences were observed in the usage of codons such as CGA, CGC, and GTC. Both Ka/Ks and p-distance were less than 1. Except for yejR, ymf57, ymf67, and ymf75, the amino acid sequence similarity between P. persalinus and U. marinum was greater than 50%. CONCLUSIONS: The mitochondrial genomes of P. persalinus and U. marinum were thoroughly compared to provide a reference for disease prevention and control. The specific PCR primers enabled us to identify P. persalinus and U. marinum rapidly and accurately at the molecular level, thus providing a basis for classification and identification.

Spectral phase effects and control requirements of coherent beam combining for ultrashort ultrahigh intensity laser systems.

Based on the premise that further improvements to the size and damage threshold of large-aperture optical components are severely limited, coherent beam combining (CBC) is a promising way to scale up the available peak power of pulses for ultrashort ultrahigh intensity laser systems. Spectral phase effects are important issues and have a significant impact on the performance of CBC. In this work, we analyze systematically factors such as spectral dispersions and longitudinal chromatism, and get the general spectral phase control requirements of CBC for ultrashort ultrahigh intensity laser systems. It is demonstrated that different orders of dispersion influence intensity shape of the combined beam, and high-order dispersions affect the temporal contrast of the combined beam, while the number of the channels to be combined has little impact on the temporal Strehl ratio (SR) of the combined beam. In addition, longitudinal chromatism should be controlled effectively since it has a detrimental effect on the combined beam at the focal plane, both temporally and spatially.

Investigation of phase effects of coherent beam combining for large-aperture ultrashort ultrahigh intensity laser systems.

Large-aperture ultrashort ultrahigh intensity laser systems are able to achieve unprecedented super-high peak power. However, output power from a single laser channel is not high enough for some important applications and it is difficult to improve output power from a single laser channel significantly in the near future. Coherent beam combining is a promising method which combines many laser channels to obtain much higher peak power than a single channel. In this work, phase effects of coherent beam combining for large-aperture ultrashort laser systems are investigated theoretically. A series of numerical simulations are presented to obtain the requirements of spatial phase for specific goals and the changing trends of requirements for different pulse durations and number of channels. The influence of wavefront distortion on coherent beam combining is also discussed. Some advice is proposed for improving the performance of combining. In total, this work could help to design a practical large-aperture ultrashort ultrahigh intensity laser system in the future.

Phase control requirements of high intensity laser beam combining.

Aiming at getting the general requirements of the beam combine for ignition scale laser facilities, the analytical expressions including the factors affecting the combine results are derived. The physical meanings of every part are illustrated. Based on these expressions, the effects of the factors, including the beam configuration, piston error, and tip/tilt error, are studied analytically and numerically. The results show that the beam configuration cannot affect the Strehl ratio (SR) of the combined beam, but it influences the FWHM of the main peak and the ratio of the main peak and the side peak. The beam separation should be no more than 1.24 times the individual beam width for the multibeam combine, and be close to the individual beam width for the two-beam combine as much as possible. The piston error can change the characteristics of the combine beam focus, including the peak intensity, the focal spot morphology, the fractional energy contained within a certain area, and the center of mass. For the two-beam combine, a piston error less than 2π/5 rad is suitable, and for the multibeam combine, the standard deviation of the piston error should be no more than 2π/10 rad. The tip/tilt error has a great influence on the combined results. It affects the superposition degree of the focal spots of the combined elements directly. A requirement of 0.5~1 µrad for the standard deviation of the tip/tilt error is adequate.

Fractional Fourier transform of flat-topped multi-Gaussian beams.

The fractional Fourier transform (FRFT) of the flat-topped multi-Gaussian beam (FMGB) is investigated based on the three kinds of FRFT optical systems: Lohmann I, Lohmann II, and quadratic graded-index systems. The analytical expressions for the FRFT of the FMGB are derived based on the propagation of the FMGB through the three systems. By introducing a hard-edge aperture function, the analytical expressions for the FRFT of the FMGB carried out by the apertured FRFT optical systems are presented. The FRFT characteristics of the FMGB for the three kinds of FRFT optical systems with and without apertures are discussed in detail. Results show that the three types of FRFT optical systems have the same function when the apertures are ignored but that significantly different characteristics are exhibited when the apertures appear.

Propagation of flat-topped multi-Gaussian beams through an apertured ABCD optical system.

The generalized analytical expression for the propagation of flat-topped multi-Gaussian beams through a misaligned apertured ABCD optical system is derived. Using this analytical expression, the propagation characteristics of flat-topped multi-Gaussian beams through a spatial filter are investigated. The analytical formula of the electric field distribution in the focal plane is also derived for revealing the effects of the misalignment parameters clearly. It is found that different misalignment parameters have different influences on the electric field distributions of the beam focus spot and the output beam characteristics. The intensity distribution of the beam is mainly determined by the misalignment matrix element E, and the phase distribution is affected by the misalignment matrix elements G and E.

Characteristics of beam alignment in a high power four-pass laser amplifier.

Beam alignment is used to control the pointing, rotation, and position of a beam automatically. We give an overview of the beam alignment system for a four-pass amplifier system. The coupling relationships between dependent quantities and deviations thereof for parameters of key optical elements are analyzed using matrix optics techniques. The rotation characteristics of a near field are discussed. The characteristics of the four-pass adjustment in the cavity spatial filter are shown and the output characteristics are provided. Finally, we develop an adjustment procedure.