AntDAS-DDA: A New Platform for Data-Dependent Acquisition Mode-Based Untargeted Metabolomic Profiling Analysis with Advantage of Recognizing Insource Fragment Ions to Improve Compound Identification.

Data-dependent acquisition (DDA) mode in ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) can provide massive amounts of MS1 and MS/MS information of compounds in untargeted metabolomics and can thus facilitate compound identification greatly. In this work, we developed a new platform called AntDAS-DDA for the automatic processing of UHPLC-HRMS data sets acquired under the DDA mode. Several algorithms, including extracted ion chromatogram extraction, feature extraction, MS/MS spectrum construction, fragment ion identification, and MS1 spectrum construction, were developed within the platform. The performance of AntDAS-DDA was investigated comprehensively with a mixture of standard and complex plant data sets. Results suggested that features in complex sample matrices can be extracted effectively, and the constructed MS1 and MS/MS spectra can benefit in compound identification greatly. The efficiency of compound identification can be improved by about 20%. AntDAS-DDA can take full advantage of MS/MS information in multiple sample analyses and provide more MS/MS spectra than single sample analysis. A comparison with advanced data analysis tools indicated that AntDAS-DDA may be used as an alternative for routine UHPLC-HRMS-based untargeted metabolomics. AntDAS-DDA is freely available at http://www.pmdb.org.cn/antdasdda.

Effects of chemical factors on the infectivity of Decapod iridescent virus 1 (DIV1).

The effects of chemical factors on the infectivity of DIV1 have not been fully accessed yet. In order to investigate the stability of DIV1 to strong brine, pH, and other chemical conditions, we conducted a bioassay using clinically healthy Penaeus vannamei individuals. DIV1 inoculum was exposed to various chemical conditions, and the infectivity of DIV1 was determined through intramuscular injection. The results showed that DIV1 lost its infectivity when exposed to strong brine, specifically in a 3 mol/L NaCl solution for a duration of 1 h. Moreover, DIV1 was found to be inactivated within 1 h when subjected to pH levels below 3.1 or above 9.6. Additionally, both Triton X-100 and 1 % formaldehyde demonstrated the ability to inactivate DIV1. These results provide valuable insights into the tolerance of DIV1 towards certain chemical factors, serving as a reference for the establishment of biosecurity measures against DIV1.

Design, Synthesis and Molecular Docking of 1,3,4-Oxadiazole-2(3H)-thione Derivatives Containing 1,4-Benzodioxane Skeleton as Potential FabH Inhibitors.

Fatty acid biosynthesis is essential for bacterial survival. Of these promising targets, ß-ketoacyl-acyl carrier protein (ACP) synthase III (FabH) is the most attractive target. A series of novel 1,3,4-oxadiazole-2(3H)-thione derivatives containing 1,4-benzodioxane skeleton targeting FabH were designed and synthesized. These compounds were determined by 1 H-NMR, 13 C-NMR, MS and further confirmed by crystallographic diffraction study for compound 7m and 7n. Most of the compounds exhibited good inhibitory activity against bacteria by computer-assisted screening, antibacterial activity test and E. coli FabH inhibitory activity test, wherein compounds 7e and 7q exhibited the most significant inhibitory activities. Besides, compound 7q showed the best E. coli FabH inhibitory activity (IC50 =2.45 µΜ). Computational docking studies also showed that compound 7q interacts with FabH critical residues in the active site.

A TaqMan probe based real-time PCR for the detection of Decapod iridescent virus 1.

Decapod iridescent virus 1 (DIV1) was proven to be the aetiological agent of a disease causing mass die-offs of shrimp, prawn and crayfish. The specific purpose of this study was to develop a new sensitive real-time PCR method for the specific detection of DIV1. A pair of primers that amplify a 142 bp fragment and a TaqMan probe were selected for the major capsid protein gene of DIV1. They were shown to be specific for DIV1 and did not react with other common shrimp pathogens or healthy shrimp DNA. The method could detect as virus levels as low as 1.2 copies of DIV1 plasmid DNA.

[Study on reflectance spectra morphological character of the hyperspectral mixed pixels at different component proportion].

Under the experimental condition, the hyperspectral reflectance spectra of the mixed pixel of lotus and water body were acquired using the multi-angles dichotic reflex platform and ASD spectrum instrument. The reflectance spectral morphological character index variation of the hyperspectral mixed pixel at different component proportion was analyzed. The conclusions are as follows: the correlation between these morphological indexes was obvious, and the best morphological index was chosen by removing the index whose R2 was greater than 0.5 (R is correlation coefficient); the variation of different morphological index was obvious; the cluster analysis shows that there was a critical value in the progress of the transformation from the pure pixel (water) to mixed pixel. If the proportion was less than the critical value, the reflectance spectra reflected the reflection characteristics of pure pixel; otherwise, it was the reflection of characteristics of mixed pixel.

The Microbiota-Dependent Treatment of Wuzhuyu Decoction for Chronic Migraine Model Rat Associated with Anxiety-Depression Like Behavior.

We previously found that Wuzhuyu Decoction (WZYD) could affect central and peripheral 5-HT to relieve hyperalgesia in chronic migraine (CM) model rats, possibly related to gut microbiota. However, the exact role of gut microbiota has not been elucidated. Accumulating evidence points to the possibility of treating central nervous system disease via the gut-brain axis. In our study, the inflammatory soup-induced CM model rats presented depression- and anxiety-like behaviors which both related to insufficient 5-HT. It was found that antibiotic administration caused community dysbiosis, and proteobacteria became the main dominant bacteria. The bacteria related to short-chain fatty acids and 5-HT generation were reduced, resulting in reduced levels of 5-HT, tryptophan hydroxylase, and secondary bile acids. Functional prediction-revealed sphingolipid signaling pathway in CM rats was significantly decreased and elevated after WZYD treatment. The effect of WZYD could be weakened by antibiotics. The CM rats exhibited anxiety- and depression-like behavior with 5-HT and number of neurons decreased in the CA1 and CA2 regions of hippocampal. The treatment of WZYD could recover to varying degrees. Antibiotics combined with WZYD attenuate the effect of WZYD on increasing the 5-HT content and related protein expression in the brain stem, plasma and colon, reducing CGRP, c-Fos, and inflammatory factors. And antibiotics also led to colon length increasing and stool retention, so that the antimigraine effect was weakened compared with WZYD. This experiment revealed that gut microbiota mediated WZYD treatment of CM rats with anxiety-depression like behavior.

A chemometric strategy to automatically screen selected ion monitoring ions for gas chromatography-mass spectrometry-based pseudotargeted metabolomics.

The pseudotargeted metabolomics based on gas chromatography-mass spectrometry (GC-MS) has the advantage of filtering out artifacts originating from sample treatment and accurately quantifying underlying compounds in the analyzed samples. However, this technique faces the problem of selecting high-quality selective ions for performing selected ion monitoring (SIM) on instruments. In this work, we proposed AntDAS-SIMOpt, an automatic untargeted strategy for SIM ion optimization that was accomplished on the basis of an experimental design combined with advanced chemometric algorithms. First, a group of diluted quality control samples was used to screen underlying compounds in samples automatically. Ions in each of the resolved mass spectrum were then evaluated by using the developed algorithms to identify the SIM ion. A Matlab graphical user interface (GUI) was designed to facilitate routine analysis, which can be obtained from http://www.pmdb.org.cn/antdassimopt. The performance of the developed strategy was comprehensively investigated by using standard and complex plant datasets. Results indicated that AntDAS-SIMOpt may be useful for GC-MS-based metabolomics.

Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure.

G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.