Rapid detection of sweepoviruses through lateral flow dipstick-based recombinase polymerase amplification.

Sweepoviruses represent a phylogenetic group of begomoviruses that cause significant sweet potato (Ipomoea batatas) production losses in various countries across the world. For rapid identification of sweepoviruses, we developed a technique based on isothermal recombinase polymerase amplification in conjunction with lateral flow dipsticks (RPA-LFD). The optimum reaction conditions for the RPA were 20 min incubation at 37°C. The RPA-LFD specifically detected distinct sweepovirus species, with no other viruses infecting sweet potato causing a cross-reaction. The detection limit of the RPA-LFD was 1.0×104 copies of the target DNA molecule per reaction, and it exhibited a 10-fold greater sensitivity than the conventional PCR. Furthermore, when coupled with an alkaline polyethylene glycol-based crude genomic DNA extraction, the entire procedure was completed in 30 min without the use of any special instruments other than a water bath. Therefore, the RPA-LFD technique is a potential sweepovirus diagnostic tool that can be used in the field with fewer available resources. Keywords: detection; sweepoviruses; recombinase polymerase amplification; lateral flow dipstick.

Fourier transform infrared spectroscopy microscopic imaging classification based on multifractal methods.

Multifractal analysis (MFA) based on generalized concepts of fractals has been applied to biological tissues composed of complex structures. In this paper, a new MFA methodology based on the neighborhood spatial correlation (NSC) is proposed for an extracting texture feature. NSC is used to extract spatial features, and the obtained spatial features are combined with spectral features of characteristic absorption peaks (CAPs) to promote more feature information. This spatial-spectral structure is used as a feature to differentiate cholesterol from Fourier transform infrared spectroscopy microscopic imaging of a rabbit artery by a support vector machine classifier. The dataset was collected between 4000 and 720 cm-1 on rabbit arteries as research objects. The experimental results show that the accuracy of the proposed spatial-spectral structure is higher than that of other multivariate analysis methods (PCA and 2DPCA). The NSC method, compared to the bottom interface method, new bottom interface method, variance method multi-weight method, and neighborhood spatial correlation method, could effectively reduce the influence of speckle noise, and the convergence rate of the weight factor q is not increased.

Research on the Attenuation Characteristics of High-Frequency Elastic Waves in Rock-Like Material.

In order to study the frequency-dependent attenuation characteristics of high-frequency elastic waves in rock-like materials, we conducted high-frequency elastic wave attenuation experiments on marble, granite, and red sandstone rods, and investigated the frequency dependence of the attenuation coefficient of high-frequency elastic waves and the frequency dependence of the attenuation of specific frequency components in elastic waves. The results show that, for the whole waveform packet of the elastic wave signal, the attenuation coefficient and the elastic wave frequency have an approximate power relationship, with the exponents of this power function being 0.408, 0.420, and 0.384 for marble, granite, and red sandstone, respectively, which are close to 1/2 the exponent value obtained theoretically by the Kelvin-Voigt viscoelastic model. However, when the specific frequency components are tracked during the elastic wave propagation, the exponents of the power relationship between the attenuation coefficient and frequency are 0.982, 1.523, and 0.860 for marble, granite, and red sandstone, respectively, which indicate that the relationship between the attenuation coefficient and frequency is rock-type dependent. Through the analysis of rock microstructure, we demonstrate that this rock-type-dependent relationship is mainly caused by the scattering attenuation component due to the small wavelength of the high-frequency elastic wave. Therefore, the scattering attenuation component may need to be considered when the Kelvin-Voigt model is used to describe high-frequency elastic wave attenuation in rock-like materials. The results of this research are of good help for further understanding the attenuation characteristics of high-frequency elastic waves in rock-like materials.

An efficient papaya leaf distortion mosaic potyvirus vector for virus-induced gene silencing in papaya.

Papaya (Carica papaya L.) is regarded as an excellent model for genomic studies of tropical trees because of its short generation time and its small genome that has been sequenced. However, functional genomic studies in papaya depend on laborious genetic transformations because no rapid tools exist for this species. Here, we developed a highly efficient virus-induced gene silencing (VIGS) vector for use in papaya by modifying an artificially attenuated infectious clone of papaya leaf distortion mosaic virus (PLDMV; genus: Potyvirus), PLDMV-E, into a stable Nimble Cloning (NC)-based PLDMV vector, pPLDMV-NC, in Escherichia coli. The target fragments for gene silencing can easily be cloned into pPLDMV-NC without multiple digestion and ligation steps. Using this PLDMV VIGS system, we silenced and characterized five endogenous genes in papaya, including two common VIGS marker genes, namely, phytoene desaturase, Mg-chelatase H subunit, putative GIBBERELLIN (GA)-INSENSITIVE DWARF1A and 1B encoding GA receptors; and the cytochrome P450 gene CYP83B1, which encodes a key enzyme involved in benzylglucosinolate biosynthesis. The results demonstrate that our newly developed PLDMV VIGS vector is a rapid and convenient tool for functional genomic studies in papaya.

A cassava common mosaic virus vector for virus-induced gene silencing in cassava.

BACKGROUND: Cassava is an important crop for food security and industry in the least-developed and developing countries. The completion of the cassava genome sequence and identification of large numbers of candidate genes by next-generation sequencing provide extensive resources for cassava molecular breeding and increase the need for rapid and efficient gene function analysis systems in cassava. Several plant virus-induced gene silencing (VIGS) systems have been developed as reverse genetic tools for rapid gene function analysis in cassava. However, these VIGS vectors could cause severe viral symptoms or inefficient gene silencing. RESULTS: In this study, we constructed agroinfection-compatible infectious cDNA clones of cassava common mosaic virus isolate CM (CsCMV-CM, genus Potexvirus, family Alphaflexiviridae) that causes systemic infection with mild symptoms in cassava. CsCMV-CM was then modified to a viral vector carrying the Nimble cloning frame, which facilitates the rapid and high-throughput cloning of silencing fragments into the viral genome. The CsCMV-based vector successfully silenced phytoene desaturase (PDS) and magnesium chelatase subunit I (ChlI) in different cassava varieties and Nicotiana benthamiana. The silencing of the ChlI gene could persist for more than two months. CONCLUSIONS: This CsCMV-based VIGS system provides a new tool for rapid and efficient gene function studies in cassava.