Ultrafast two-dimensional imaging for surface defects measurement of mirrors based on a virtually imaged phased-array.

Single-shot measurement of surface defects of mirrors is vital for monitoring the operating states of high power lasers systems. While conventional methods suffer from low speed and small dynamic range. Here, we demonstrate a method for high speed two-dimensional (2D) surface amplitude-type defects measurement based on ultrafast single-pixel imaging assisted by a virtually imaged phased-array. Together with an optical grating, 2D wavelength to space mapping is achieved based on Fraunhofer far field diffraction, and the uniform broad spectrum of a home-made dissipative soliton is uniformly dispersed into the targeted mirror with one-to-one wavelength-to-space mapping. The surface amplitude-type defects are modulated into the intensity variation of the reflected spectrum. Then, we build a dispersive Fourier transform module for wavelength to time mapping, through which modulated spectral information is time stretched into the temporal domain, and recorded by a high speed photodetector together with a real time oscilloscope. Finally, to diminish the distortions induced by nonlinear dispersion during the wavelength-time mapping, we utilize the interpolation, and reconstruct the 2D surface with a frame rate of 7.6 MHz. A two-dimensional image with widths of 1.5 × 2 mm can be obtained within 10 ns, with a y direction spatial resolution of 180 µm and a x direction spatial resolution of 140 µm. This ultrafast 2D surface defects measurement scheme is promising for real-time monitoring of surface defects mirrors with large aperture, which are widely utilized in various high power laser systems.

High speed surface defects detection of mirrors based on ultrafast single-pixel imaging.

High speed surface defects detection of mirrors is of great significance, for detecting the quality of the mirrors on-site, and ultimately for monitoring the operating states of laser systems. The speeds of conventional proposals are relatively low as they utilize mechanically scanning methods or two-dimensional charge-coupled devices. Here, we propose a high speed surface detection method based on ultrafast single-pixel imaging, which consists of a spatial Fourier optical module for frequency-space mapping and a dispersive Fourier transform module for frequency-time mapping. An optical grating is utilized to map the wideband spectrum of dissipative soliton into the spatial domain under far-field diffraction, where the mirror is inspected. Dispersive Fourier transform is used to map the surface-defects-coded spectral information into the temporal domain, then recorded by a high speed single-pixel detector. The detection system permits continuous single-shot spectra measurement with a frame rate equivalent to the pulse repetition rate (8.4 MHz). We extract amplitude defects by demodulating light intensity, and obtain phase defects by demodulating the interference spectrum with a Mach-Zehnder interferometer structure. Experimental results show that the damaged mirror with a two-dimensional width of 10 × 13 mm can be obtained with a spatial resolution of 90 µm. The obtained phase accuracy after Hilbert transformation is 0.00217 rad, corresponding to a depth resolution of 51 nm. This scheme can find promising applications for surface defects detection of large aperture mirrors, and real-time monitoring of laser systems with high energy.

A multigene phylogentic analysis of Potato virus Y and its application in strain identification.

The objective of this study is to develop a rapid and accurate multigene phylogenetic analysis to identify Potato virus Y (PVY) strains. The phylogenetic relationships of strains within the PVY species were evaluated with isolate-strain association using five datasets of concatenated sequences from the P1, HC-pro, VPg and CP genes to determine the best dataset for PVY strain identification. Results from phylogenetic analyses and Bayesian tip-association significance (BaTS) tests indicated that the major PVY strains could be distinguished using the P1, VPg and CP concatenated sequences datasets but not the remaining concatenated sequence datasets. Phylogenetic trees reconstructed from the concatenated sequences of P1, VPg and CP genes revealed that the ML and NJ trees had broadly similar topologies and that both were better than the maximum clade credibility tree (MCC). Additionally, the full genome of HLJ26, one isolate randomly selected for the multigene phylogenetic analysis, was clustered with high confidence among members of the PVYNTN-NW (SYR-Ⅱ) strain, which includes isolates of SYR-Ⅱ-2-8, SYR-Ⅱ-Be1 and SYR-Ⅱ-DrH. This suggests that it was a PVYNTN-NW (SYR-Ⅱ) isolate. Recombination analysis of this isolate identified four putative recombination joints in the P1, HC-pro/P3, VPg and the 5'-terminus of CP. This pattern is similar to that observed in the genomic structure of PVYNTN-NW (SYR-I), supporting the classification of this isolate as the PVYNTN-NW strain (SYR-Ⅱ). Simultaneously, two expected fragments of approximately 1 000 and 400 bp in size were also amplified from the isolate by a multiplex RT-PCR, consistent with the expected band pattern of the PVYNTN-NW (SYR-Ⅱ) strain. This further supports the utility of the multigene phylogenetic method in identifying PVY strains. We propose that the major PVY strains could be distinguished accurately using multigene phylogenetic analysis based on the concatenated sequences from the P1, VPg and CP genes.

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan.

Potato virus Y (PVY) is an important plant pathogen causing considerable economic loss to potato production. Knowledge of the population genetic structure and evolutionary biology of the pathogen, particularly at a transnational scale, is limited but vital in developing sustainable management schemes. In this study, the population genetic structure and molecular evolution of PVY were studied using 127 first protein (P1) and 137 coat protein (CP) sequences generated from isolates collected from potato in China and Japan. High genetic differentiation was found between the populations from the two countries, with higher nucleotide diversity in Japan than China in both genes and a KST value of .216 in the concatenated sequences of the two genes. Sequences from the two countries clustered together according to their geographic origin. Further analyses showed that spatial genetic structure in the PVY populations was likely caused by demographic dynamics of the pathogen and natural selection generated by habitat heterogeneity. Purifying selection was detected at the majority of polymorphic sites although some clade-specific codons were under positive selection. In past decades, PVY has undergone a population expansion in China, whereas in Japan, the population size of the pathogen has remained relatively constant.

Geographically driven adaptation of chilli veinal mottle virus revealed by genetic diversity analysis of the coat protein gene.

Chilli veinal mottle virus (ChiVMV) is an important plant pathogen with a wide host range. The genetic structure of ChiVMV was investigated by analyzing the coat protein (CP) genes of 87 ChiVMV isolates from seven Asian regions. Pairwise F ST values between ChiVMV populations ranged from 0.108 to 0.681, indicating a significant spatial structure for this pathogen. In phylogeny-trait association analysis, the viral isolates from the same region tended to group together, showing a distinct geographic feature. These results suggest that geographic driven adaptation may be an important determinant of the genetic diversity of ChiVMV.

[Comparative analysis of population genetic structure of Potato virus Y from different hosts].

Nucleotide sequences of P3 and pipo genes of Potato virus Y (PVY) from potato and tobacco were compared to investigate the effect of hosts on the population genetic structure. Meanwhile, mutation, natural selection and gene flow were evaluated to determine evolutionary forces responsible for the population genetic dynamics. The fixation indices of population differentiation (FST) of PVY from tobacco and potato were 0.116 and 0.120, respectively with significant difference, suggesting a moderate genetic differentiation between the two populations. Genetic variation analysis showed that nucleotide identities in P3 and pipo genes among the viral isolates from tobacco were respectively in the range of 85.2%-100% and 76.5%-100% while that from potato were respectively in the range of 95.7%-100% and 93.0%-100%, indicating higher genetic variation in PVY from tobacco than that from potato. Moreover, purifying selection was detected on the majority of polymorphic sites within P3 gene, suggesting that most of mutations in the gene were harmful and consequently being eliminated by natural selection. Conversely, positive selection was detected on two polymorphic sites, suggesting that these two mutations were beneficial to PVY. Neither purifying nor positive selection was detected in pipo gene, indicating neutral evolution of the gene. The values of gene flow (Nm) between PVY populations from tobacco and potato in P3 and pipo genes were 1.91 and 1.83, respectively, suggesting strong gene flow also contributes significantly to the population genetic dynamics of PVY population. In summary, this study indicates there was a significant genetic variation in PVY hosted by tobacco and potato, and mutation, natural selection and gene flow all contribute to the genetic diversity and population dynamic of the virus.

Probiotic Bacillus pumilus SE5 shapes the intestinal microbiota and mucosal immunity in grouper Epinephelus coioides.

The health benefits of probiotics are thought to occur, at least in part, through an improved intestinal microbial balance in fish, although the molecular mechanisms whereby probiotics modulate the intestinal microbiota by means of activation of mucosal immunity are rarely explored. In this study, the effects of viable and heat-inactivated probiotic Bacillus pumilus SE5 on the intestinal dominant microbial community and mucosal immune gene expression were evaluated. The fish were fed for 60 d with 3 different diets: control (without probiotic), and diets T1 and T2 supplemented with 1.0 × 108 cells g⁻¹ viable and heat-inactivated B. pumilus SE5, respectively. Upregulated expression of TLR1, TLR2 and IL-8, but not MyD88 was observed in fish fed the viable probiotic, while elevated expression of TLR2, IL-8 and TGF-ß1, but not MyD88 was observed in fish fed the heat-inactivated B. pumilus SE5. The induced activation of intestinal mucosal immunity, especially the enhanced expression of antibacterial epinecidin-1, was consistent with the microbial data showing that several potentially pathogenic bacterial species such as Psychroserpens burtonensis and Pantoea agglomerans were suppressed by both the viable and heat-inactivated probiotic B. pumilus SE5. These results lay the foundation for future studies on the molecular interactions between probiotics, intestinal microbiota and mucosal immunity in fish.