Photochromic visual sensing chip for isothermal amplification detection of porcine transmissible gastroenteritis virus.

The outbreak of transmissible gastroenteritis virus (TGEV) will cause huge economic losses to the whole pig industry. Hence, there is urgent need to develop a rapid and ultrasensitive method for detection of TGEV. As a nucleic acid detection technique, loop-mediated isothermal amplification (LAMP) can achieve quantitative detection of targeted nucleic acids with high sensitivity and selectivity. Nevertheless, the signal outputs of LAMP method must be acquired by complicated instruments. In this work, we firstly developed a LAMP photochromic sensing chip for porcine TGEV detection by combination of the photochromic sensing chip and nucleic acid amplification. The detection signal was based on color change of electrochromic material rather than electrical signal, and thus the detection signal can be obtained by visualization without relying on complicated instrument. The entire test was performed with small fluorinated indium tin oxide electrodes modified with zinc oxide (ZnO) (a photocatalytic material) and Prussian blue (PB) (an electrochromic material). When photoinduced electrons produced by ZnO were injected into PB under light, the PB was reduced to Prussian white. The higher the concentration of TGEV, the more double-stranded DNA was produced after amplification. The amplified product produced greater impedance, and fewer electron was transferred, which affect the corresponding color change of PB. The sensing chip also showed highly sensitive response to TGEV, with the minimum limit of detection was determined to be 2.5 fg/µL. The sensing chip developed herein will provide a new avenue for DNA amplification detection by visualization.

Characterization of an aspartate aminotransferase encoded by YPO0623 with frequent nonsense mutations in Yersinia pestis.

Yersinia pestis, the causative agent of plague, is a genetically monomorphic bacterial pathogen that evolved from Yersinia pseudotuberculosis approximately 7,400 years ago. We observed unusually frequent mutations in Y. pestis YPO0623, mostly resulting in protein translation termination, which implies a strong natural selection. These mutations were found in all phylogenetic lineages of Y. pestis, and there was no apparent pattern in the spatial distribution of the mutant strains. Based on these findings, we aimed to investigate the biological function of YPO0623 and the reasons for its frequent mutation in Y. pestis. Our in vitro and in vivo assays revealed that the deletion of YPO0623 enhanced the growth of Y. pestis in nutrient-rich environments and led to increased tolerance to heat and cold shocks. With RNA-seq analysis, we also discovered that the deletion of YPO0623 resulted in the upregulation of genes associated with the type VI secretion system (T6SS) at 26°C, which probably plays a crucial role in the response of Y. pestis to environment fluctuations. Furthermore, bioinformatic analysis showed that YPO0623 has high homology with a PLP-dependent aspartate aminotransferase in Salmonella enterica, and the enzyme activity assays confirmed its aspartate aminotransferase activity. However, the enzyme activity of YPO0623 was significantly lower than that in other bacteria. These observations provide some insights into the underlying reasons for the high-frequency nonsense mutations in YPO0623, and further investigations are needed to determine the exact mechanism.

Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities.

The bacterium Yersinia pestis has developed various strategies to sense and respond to the complex stresses encountered during its transmission and pathogenic processes. PurR is a common transcriptional regulator of purine biosynthesis among microorganisms, and it modulates the transcription level of the pur operon to suppress the production of hypoxanthine nucleotide (IMP). This study aims to understand the functions and regulatory mechanisms of purR in Y. pestis. Firstly, we constructed a purR knockout mutant of Y. pestis strain 201 and compared certain phenotypes of the null mutant (201-ΔpurR) and the wild-type strain (201-WT). The results show that deleting purR has no significant impact on the biofilm formation, growth rate, or viability of Y. pestis under different stress conditions (heat and cold shock, high salinity, and hyperosmotic pressure). Although the cytotoxicity of the purR knockout mutant on HeLa and 293 cells is reduced, the animal-challenging test found no difference of the virulence in mice between 201-ΔpurR and 201-WT. Furthermore, RNA-seq and EMSA analyses demonstrate that PurR binds to the promoter regions of at least 15 genes in Y. pestis strain 201, primarily involved in purine biosynthesis, along with others not previously observed in other bacteria. Additionally, RNA-seq results suggest the presence of 11 potential operons, including a newly identified co-transcriptional T6SS cluster. Thus, aside from its role as a regulator of purine biosynthesis, purR in Y. pestis may have additional regulatory functions.

Accurate and ultrasensitive detection for PEDV based on photoelectrochemical sensing coupling loop-mediated isothermal amplification.

Porcine epidemic diarrhea (PED) is a serious disease requiring a simple and accurate detection method. Accordingly, this study developed a novel, ultrasensitive photoelectrochemical (PEC) sensing platform using the loop-mediated isothermal amplification (LAMP) technique (LAMP-PEC). An amino (-NH2)-modified LAMP product is obtained by amplification of the PED virus gene with specially designed primers. The generated NH2-modified LAMP product is assembled on the surface of an electrode by forming imine linkages between aldehyde and amino groups based on the Schiff base reaction. A stable photocurrent is provided by a CdIn2S4 photoactive material, which possesses high photoelectric conversion efficiency. Amplified DNA assembled on the electrode surface increases steric hindrance and hinders electrons from moving from the electrode to electron acceptors, which decreases the photocurrent. This strategy can detect PEDV with a low detection limit of 0.3 fg µL-1 and a wide linear range of 1 × 10-3-1 × 102 pg/µL. The sensing platform has excellent specificity and sensitivity and can be used for the quantitative detection of many other pathogens with the assistance of LAMP.

Development and evaluation of a multiplex droplet digital polymerase chain reaction method for simultaneous detection of five biothreat pathogens.

Biothreat agents pose a huge threat to human and public health, necessitating the development of rapid and highly sensitive detection approaches. This study establishes a multiplex droplet digital polymerase chain reaction (ddPCR) method for simultaneously detecting five high-risk bacterial biothreats: Yersinia pestis, Bacillus anthracis, Brucella spp., Burkholderia pseudomallei, and Francisella tularensis. Unlike conventional multiplex real-time PCR (qPCR) methods, the multiplex ddPCR assay was developed using two types of probe fluorophores, allowing the assay to perform with a common two-color ddPCR system. After optimization, the assay performance was evaluated, showing a lower limit of detection (LOD) (0.1-1.0 pg/µL) and good selectivity for the five bacteria targets. The multiplex assay's ability to simultaneously detect two or more kinds of targets in a sample was also demonstrated. The assay showed strong sample tolerance when testing simulated soil samples; the LOD for bacteria in soil was 2 × 102-2 × 103 colony-forming unit (CFU)/100 mg soil (around 5-50 CFU/reaction), which was 10-fold lower than that of the single-target qPCR method. When testing simulated soil samples at bacterial concentrations of 2 × 103-2 × 104 CFU/100 mg soil, the assay presented a higher sensitivity (100%, 35/35) than that of the qPCR method (65.71%, 23/35) and a good specificity (100%, 15/15). These results suggest that the developed 5-plex ddPCR method is more sensitive than conventional qPCR methods and is potentially suitable for rapidly detecting or screening the five selected bacterial biothreats in suspicious samples.

Enhanced cathodic electrochemiluminescent microcystin-LR aptasensor based on surface plasmon resonance of Bi nanoparticles.

Sensitive testing for Microcystins-LR (MC-LR) is needed because of its serious environmental and human health hazards. In this work, a new type of surface plasmon resonance (SPR) enhanced cathodic electrochemiluminescence (ECL) aptasensing platform was designed in which boron and nitrogen co-doped graphene quantum dots (BN-GQDs) were used as the luminary and bismuth nanoparticles (Bi NPs) were used as the SPR source. SPR effect of non-precious metal Bi NPs can induce and enhance ECL signal of BN-GQDs because the fluorescence spectrum of BN-GQDs overlaps well with the ultraviolet-visible absorption spectrum of Bi NPs. On this basis, a sensitive sensing system based on the Bi NPs and BN-GQDs was established for MC-LR detection. The results showed that the ECL sensing signal obtained was linear with the negative logarithm of the target MC-LR concentration in the range of 0.01-5000 pM, and the detection limit was 0.003 pM. In addition, the sensor had high stability and good reproducibility, which can be applied to the detection of MC-LR in actual samples. The method had good specificity and can not be disturbed by its homolog, which can be used for sensitive and reliable detection of complex samples.

Nanoparticles-doped induced defective ZIF-8 as the novel cathodic luminophore for fabricating high-performance electrochemiluminescence aptasensor for detection of omethoate.

Although the use of omethoate (OMT) for pests control is enormously economically beneficial for agricultural production, the high toxicity of OMT to nontarget organisms has resulted in the contamination of soil, river water, and food materials. Developing sensitive and convenient techniques to detect OMT residues is vital to society. Electrochemiluminescence (ECL) is a powerful analytical tool and has been widely applied in biosensors. To boost the co-reaction efficiency and ECL intensity, we introduced defective ZIF-8 as the novel cathodic luminophore. At the same time, defect generated by the doping of MoTe2 nanoparticles into ZIF-8 could easily electrocatalytic reduce the co-reactor S2O82- to SO4•-. Hence, based on the catalysis of defective ZIF-8, the ECL intensity of MoTe2/ZIF-8 nanocomposites is much higher than both ZIF-8 and MoTe2 nanoparticles. By integration of as-prepared materials with specificity omethoate aptamer, the ECL sensor showed a broad linear range (10-10 g L-1 and 10-5 g L-1) and a comparatively low detection limit (3.3 × 10-11 g L-1). Besides, the ECL aptasensor appeared a good practical performance to detect potato and spinach extraction samples, which proposed a promising guideline for developing ECL aptasensors with high efficiency.