Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives.

Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.

Band alignment of ZnO-based nanorod arrays for enhanced visible light photocatalytic performance.

A ternary semiconductor ZnO/MoS2/Ag2S nanorod array in an intimate core-shell structure was synthesized on glass substrates. The physicochemical properties and photocatalytical performance of the specimen were characterized and compared with single ZnO and binary ZnO/Ag2S and ZnO/MoS2 nanorod arrays. It is found that the coating layers depressed the band edge emission of the ZnO core, improved light absorption in the visible range, reduced charge transfer resistance, and increased photocatalytic activity. The ternary heterojunction nanorod array possessed full solar absorption with an efficiency of 52.88% for the degradation of methylene blue under visible light in 30 min. The efficiency was higher than other arrays and was 7.6 times that of the ZnO array. Theory analysis revealed that the coating layer brought different band alignment in the heterojunctions for efficient charge separation and conduction, which was beneficial for the photocatalytic performance.

Enhanced Faraday effects of magneto-plasmonic crystals with plasmonic hexagonal hole arrays.

Magneto-optical (MO) properties of the bilayed Au/BIG and trilayered Au/BIG/Au magneto-plasmonic crystals (MPCs) were analyzed by the finite-difference time-domain method. In contrast to the low deflection angle and transmission of the smooth thin film, all the heterostructures with perforated holes in the top Au film displayed a similar trend with two strong resonant bands in Faraday rotation and transmittance in the near infrared wavelength range. The bands and electric distribution relative to the component and hole structure were revealed. The MPC with plasmonic hexagonal holes was found to own superior Faraday effects with distinctive anisotropy. The evolution of the resonant bands with the size and period of hexagonal holes, the thickness of different layers, and the incident light polarization was illustrated. The Faraday rotation of the optimized bilayed and trilayered hexagonal MPCs was improved 15.3 and 17.5 times, and the transmittance was enhanced 12.1 and 11.1 folds respectively at the resonant wavelength in comparison to the continuous Au/BIG film, indicating that the systems might find potential application in MO devices.

MicroRNA-449 targets histone deacetylase 1 to regulate the proliferation, invasion, and apoptosis of synovial fibroblasts in rheumatoid arthritis.

BACKGROUND: Rheumatoid arthritis (RA) is a chronic joint disease. The study aimed to explore the effects of microRNA (miR)-449 and histone deacetylase 1 (HDAC1) on the proliferation, invasion, and apoptosis of synovial fibroblasts in rheumatoid arthritis. METHODS: Synovial tissue was collected from 20 patients with RA and 20 patients with osteoarthritis (OA) who underwent joint replacement surgery. RA synovial fibroblasts (RASFs) and OA synovial fibroblasts (OASFs) were isolated and cultured. Real-time quantitative PCR was used to detect the expression levels of miR-449 and HDAC1 in synovial tissues and cells. Western blot was performed to detect the cellular expression levels of HDAC1 protein, and apoptosis and invasion-related proteins. The proliferation, invasion, and apoptosis of RASFs were detected by MTT assay, Transwell assay, and flow cytometry. The dual-luciferase reporter gene was used to test the targeting relationship between inflammatory miR-449 and HDAC1. RESULTS: Compared with normal synovial tissue and OASFs, the levels of HDAC1 messenger RNA in RA synovial tissue and RASF cells were significantly increased (P<0.01), while the expression levels of miR-449 were significantly decreased (P<0.01). The dual-luciferase reporter gene experiment confirmed that miR-449 could specifically bind to the 3' untranslated region of HDAC1 to inhibit its luciferase activity (P<0.05). HDAC1 inhibition or miR-449 overexpression significantly inhibited the proliferation and invasion of RASFs (P<0.001), while inducing their apoptosis (P<0.001). HDAC1 overexpression reversed the biological effects of miR-449 on RASFs (P<0.001). CONCLUSIONS: miR-449 inhibits the proliferation and invasion of RASFs and induces their apoptosis by targeting HDAC1, thereby exerting a protective effect against RA.

Recent advances and perspectives in photo-induced enhanced Raman spectroscopy.

Phototreatment is at the leading edge of a research hot topic as a driving force for structural transformation, spectral and electromagnetism improvements, and the functional performance of nanomaterials. Light irradiation can excite surface plasmons in noble metal nanoparticles, create electron-hole pairs, and produce charge transfer in semiconductor substrates, which have led to it being widely used in surface-enhanced Raman spectroscopy (SERS) for life sciences, environmental protection, and biological analysis. Photo-induced enhanced Raman spectroscopy (PIERS) is a new technology developed on the basis of traditional SERS and has proven to be an efficient way to resolve several critical challenges thanks to its incomparable superiority for incontiguous operation, efficient charge separation and enrichment, and a large signal enhancement for a wide range of biomolecules at the trace level. This makes PIERS a powerful technique with very appealing and promising applications in various branches of analytical science. In this review, the enhancement mechanisms of PIERS are analyzed in comparison with SERS. Afterward, the parameters influencing the enhancement of PIERS, including the substrate, light irradiation, and relaxation are discussed in detail. Finally, some perspectives on further developments of PIERS are exemplified. The PIERS technique will continue to evolve and grow with new developments and its successful application in bioanalysis and life sciences.

Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication.

The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

Tumor necrosis factor receptor-associated factor 6 (TRAF6) inhibition modulates bone loss and matrix metalloproteinase expression levels in collagen-induced rheumatoid arthritis rat.

BACKGROUND: Rheumatoid arthritis (RA) is a main characterized by persistent synovitis, systemic inflammation, and autoantibodies. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an E3 ubiquitin ligase and is a crucial cytoplasm signal adaptor that can regulate critical biological processes. This research aims to explore the function of TRAF6 on bone loss and matrix metalloproteinase (MMP) expression in collagen-induced RA rats. METHODS: The RA model in rats (Sprague Dawley rat, 5-6 weeks old, weight 246.88±8.31 g) was set up via using collagen-induced RA. The shRNA-TRAF6 knockdown efficiency was tested using real-time reverse transcription-polymerase chain reaction (qRT-PCR) and western blot, respectively. The rats were divided into four groups: the control group, RA group, RA + shRNA-NC group, and RA + TRAF6-shRNA group. The tartrate-resistant acidic phosphatase (TRAP), hematoxylin and eosin (H&E), and Saffron O staining were employed to test the bone injury. The mRNA and protein expressive of Osteoclast-associated receptor (OSCAR), TRAP, Osterix (Osx), Collagen type I alpha 1 (COL1A1), Distal-less homeobox2 (Dlx2), tissue inhibitor of metalloproteinase (TIMP), matrix metalloproteinase-1(MMP-1), Cyclooxygenase 2 (COX2) and qRT-PCR performed MMP-13 and western blot, respectively. RESULTS: The mRNA and protein expression levels of TRAF6 were down-regulated in the RA + TRAF6- shRNA group. After the levels of TRAF6 were inhibited, the levels of bone volume/total volume (BV/TV), trabecular bone thickness (Tb.Th), and trabecular bone number (Tb.N) were increased, while the levels of trabecular bone space (Tb.Sp), Osteocalcin and ALP were deceased. The mRNA and protein expression levels of OSCAR, TRAP, MMP-1, COX2, and MMP-13 were reduced obviously in the RA + TRAF6- shRNA group compared with the RA + shRNA-NC group, while the levels of TIMP-1, OSX, CoL1A1, and DLx2 were enhanced obviously. CONCLUSIONS: Inhibition of TRAF6 reduces bone loss and MMP expression levels in collagen-induced RA rat, and supplies an alternative treatment method in RA.

Exploring the computational methods for protein-ligand binding site prediction.

Proteins participate in various essential processes in vivo via interactions with other molecules. Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has great significance for drug discoveries. Therefore, predicting protein-ligand binding sites has long been under intense research in the fields of bioinformatics and computer aided drug discovery. In this review, we first introduce the research background of predicting protein-ligand binding sites and then classify the methods into four categories, namely, 3D structure-based, template similarity-based, traditional machine learning-based and deep learning-based methods. We describe representative algorithms in each category and elaborate on machine learning and deep learning-based prediction methods in more detail. Finally, we discuss the trends and challenges of the current research such as molecular dynamics simulation based cryptic binding sites prediction, and highlight prospective directions for the near future.

[A method for determination of trace naphthalene and phenanthrene in water using constant-wavelength synchronous fluorescence spectrometry].

In view of synchronous fluorescence possessing the character of good selectivity, high sensitivity, less interference, etc. it can be used for simultaneous determination of multi-component mixtures of polycyclic aromatic hydrocarbons (PAHs). A new method of constant-wavelength synchronous fluorescence spectrometry to determine two naphthalene and phenanthrene of PAHs was developed in this study. The effect of different experimental conditions, such as different disolvents for character of fluorescence spectra and the choose of the optimal wavelength difference were studied. Experiment showed that the simultaneous indentification and quantitative determination of the two PAHs when delta lambda = 100 was chosen. The fluorescence intensity was linearly related to naphthalene and phenanthrene concentration in the range of 0.5-25.0 microg x L(-1) with correlation coefficient 0.999 5 and 0.999 7, respectively. The detection limits were all lower than 0.03 microg x L(-1), and the relative standard deviations for naphthalene and phenanthrene were 1.19% and 180% (n=7), respectively. Results show that the compounds can be analyzed qualitatively and quantitatively by synchronous fluorescence spectrometry.

[Synthesis and spectral studies of functionalized L-Cys-CdS nanoparticles as fluorescence probes].

In this work, nano-CdS was successfully prepared. The nano-CdS was also modified with L-cysteine. Absorption and fluorescence spectra of CdS nanoparticles for different pH values, reaction times and different Cys/Cd2+/S ratios were investigated. Meanwhile a fluorescence enhancing effect was observed between trace zinc ions and the functionalized L-Cys-CdS nanoparticles. The response is linearly proportional to the concentration of zinc ions from 1.0 to 15 micromol x L(-1). The functionalized nanoparticles are hopeful of use as fluorescence probes in detecting trace elements in biological samples.