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The current knowledge of Staphylococcus warneri phages is limited, with few genomes sequenced and characterized. In this study, a prophage, vB_G30_01, isolated from Staphylococcus warneri G30 was characterized and evaluated for its lysogenic host range. The phage was studied using transmission electron microscopy and a host range. The phage genome was sequenced and characterized in depth, including phylogenetic and taxonomic analyses. The linear dsDNA genome of vB_G30_01 contains 67 predicted open reading frames (ORFs), classifying it within Bronfenbrennervirinae. With a total of 10 ORFs involved in DNA replication-related and transcriptional regulator functions, vB_G30_01 may play a role in the genetics and transcription of a host. Additionally, vB_G30_01 possesses a complete set of genes related to host lysogeny and lysis, implying that vB_G30_01 may influence the survival and adaptation of its host. Furthermore, a comparative genomic analysis reveals that vB_G30_01 shares high genomic similarity with other Staphylococcus phages and is relatively closely related to those of Exiguobacterium and Bacillus, which, in combination with the cross-infection assay, suggests possible cross-species infection capabilities. This study enhances the understanding of Staphylococcus warneri prophages, providing insights into phage–host interactions and potential horizontal gene transfer. [ABSTRACT FROM AUTHOR]

Tuberculosis (TB) is a global infectious threat, and the emergence of multidrug-resistant TB has become a major challenge in eradicating the disease that requires the discovery of new treatment strategies. This study aimed to elucidate the immune infiltration and molecular regulatory network of T cell-interacting activating receptors on myeloid cell 1 (TARM1)-related genes based on a bioinformatics analysis. The GSE114911 dataset was obtained from the Gene Expression Omnibus (GEO) and screened to identify 17 TARM1-related differentially expressed genes (TRDEGs). Genes interacting with the TRDEGs were analyzed using a Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. A gene set enrichment analysis (GSEA) was used to identify the biological pathways significantly associated with a Mycobacterium tuberculosis (Mtb) infection. The key genes were obtained based on Cytoscape's cytoHubba plug-in. Furthermore, protein–protein interaction (PPI) networks were analyzed through STRING, while mRNA–RNA-binding protein (RBP) and mRNA–transcription factor (TF) interaction networks were developed utilizing the StarBase v3.0 and ChIPBase databases. In addition, the diagnostic significance of key genes was evaluated via receiver operating characteristic (ROC) curves, and the immune infiltration was analyzed using an ssGSEA and MCPCounter. The key genes identified in the GSE114911 dataset were confirmed in an independent GSE139825 dataset. A total of seventeen TRDEGs and eight key genes were obtained in a differential expression analysis using the cytoHubba plug-in. Through the GO and KEGG analysis, it was found that these were involved in the NF-κB, PI3K/Akt, MAPK, and other pathways related to inflammation and energy metabolism. Furthermore, the ssGSEA and MCPCounter analysis revealed a significant rise in activated T cells and T helper cells within the Mtb infection group, which were markedly associated with these key genes. This implies their potential significance in the anti-Mtb response. In summary, our results show that TRDEGs are linked to inflammation, energy metabolism, and immune cells, offering fresh insights into the mechanisms underlying TB pathogenesis and supporting further investigation into the possible molecular roles of TARM1 in TB, as well as assisting in the identification of prospective diagnostic biomarkers. [ABSTRACT FROM AUTHOR]

Observational studies indicate that variations in peripheral blood mononuclear cell (PBMC) subsets are associated with an increased risk of pulmonary tuberculosis (PTB) and coronavirus disease 2019 (COVID-19), but causal validation is lacking. Here, we combined single-cell expression quantitative trait locus (sc-eQTL) and two-sample mendelian randomization (MR) analyses to elucidate the causal relationship between PBMC subsets and the occurrence of PTB and COVID-19 and verified by RT-qPCR. We observed an increase in the CD4+ Effective Memory T Cell (CD4+ TEM) cluster in both PTB and COVID-19 patients according to the single-cell transcriptional landscape of PBMC. Through MR analysis using an inverse variance weighted (IVW) method, we found strong evidence of positive correlations between CD4+ TEM cell markers (GBP2, TRAV1-2, and ODF2L) and PTB, and between markers (LAG3 and SLFN5) and COVID-19, especially highlighted by lead eQTL-SNPs of GBP2 (rs2256752, p = 4.76321 × 10−15) and LAG3 (rs67706382, p = 6.16× 10−16). Similar results were observed in validation sets, and no pleiotropy was detected in sensitivity analyses including weighted median (WM), MR-Egger, MR-pleiotropy residual sum and outlier, and leave-one-out analyses (all p > 0.05). We visualized the colocalization of marker-eQTLs and markers of PTB and COVID-19 genome-wide association study (GWAS) associations. Based on CellChat analyses, monocytes communicated predominantly with CD4+ TEM cells positively expressing PTB markers (GBP2, TRAV1-2, and ODF2L) and COVID-19 markers (LAG3 and SLFN5) in both PTB and COVID-19. Our data suggest a causal effect between two key CD4+ TEM cell markers (GBP2 and LAG3) and the risk for PTB and COVID-19 infection. Our findings provide novel insights into the biological mechanism for PTB and COVID-19 infection, but future single-cell studies are necessary to further enhance understanding of this find. [ABSTRACT FROM AUTHOR]

A dual NIR fluorescent probe Cy-ND is developed for viscosity sensing with λex/em = 766/806 nm, making it apt for biological analysis, whose response is validated through DFT and TDDFT computations. Cy-ND successfully detected viscosity changes amidst acute alcohol-induced liver injury and liver ischemia-reperfusion injury. [ABSTRACT FROM AUTHOR]

To improve the simulation performance of the RegCM4 model in climate simulations over the Yangtze River Basin (YRB), it is essential to determine the optimal cumulus convection and land surface process schemes from the numerous physical parameterization options within RegCM4. In this study, we selected five cumulus convection schemes (Kuo, Grell, Emanuel, Tiedtke, and Kain–Fritsch) and three land surface process schemes (BATS, CLM3.5, and CLM4.5) to configure 72 mixed schemes. Four years of short-term simulations (1990–1993) with a horizontal resolution of 50 km were conducted using ERA-Interim as the initial and boundary conditions for the 72 schemes. The climate simulation performance of all schemes in the YRB was comprehensively evaluated using a multi-criteria scoring approach. The results indicate that among the selected cumulus convection schemes, the Kain–Fritsch scheme, applied to both ocean and land, demonstrates optimal performance in simulating precipitation over the YRB, with spatial correlation coefficients between simulated and observed annual precipitation around 0.3. Compared to the Community Land Models (CLM3.5 and CLM4.5), BATS exhibits superior capabilities in reproducing the temperature features of the region, with spatial correlation coefficients between simulated and observed values typically exceeding 0.99 and standard deviations within 1.25 °C. Under the optimal KF scheme, the simulated soil moisture in the YRB using CLMs is notably drier, ranging from −7.79 to −8.39 kg/m2, compared to that achieved with BATS. The findings provide a localized reference for the parameterization schemes of RegCM4 in the YRB. [ABSTRACT FROM AUTHOR]

Hidden chaotic attractors is a fascinating subject of study in the field of nonlinear dynamics. Jerk systems with a stable equilibrium may produce hidden chaotic attractors. This paper seeks to enhance our understanding of hidden chaotic dynamics in jerk systems of three variables (x , y , z) with nonlinear terms from a predefined set: { − x y + d z 2 , − x y + d z tanh (z) } , where d is a real parameter. The behavior of the systems is analyzed using rigorous Hopf bifurcation analysis and numerical simulations, including phase portraits, bifurcation diagrams, Lyapunov spectra, and basins of attraction. For certain jerk systems with a subcritical Hopf bifurcation, adjusting the coefficient of a linear term can lead to hidden chaotic behavior. The adjustment modifies the subcritical Hopf equilibrium, transforming it from an unstable state to a stable one. One such jerk system, while maintaining its equilibrium stability, experiences a sudden transition from a point attractor to a stable limit cycle. The latter undergoes a period-doubling route to chaos, which may be followed by a reverse route. Therefore, by perturbing certain jerk systems with a subcritical Hopf equilibrium, we can gain insights into the formation of hidden chaotic attractors. Furthermore, adjusting the coefficient of the nonlinear term z tanh (z) in certain systems with a stable equilibrium can also lead to period-doubling routes or reverse period-doubling routes to hidden chaotic dynamics. Both findings are significant for our understanding of the hidden chaotic dynamics that can emerge from nonlinear systems with a stable equilibrium. [ABSTRACT FROM AUTHOR]

In the traditional method of the bio-fabrication of zinc oxide nanoparticles (ZnONPs), bacterial strains face metal toxicity and antimicrobial action. In the current study, an alkalescent nucleoside antibiotic was mixed with zinc hexanitrate to fabricate the ZnONPs. An integrated approach of DIAION HP-20 macroporous resin and sephadex LH-20 column chromatography was adopted to separate and purify alkalescent nucleoside AN03 from Streptomyces koyanogensis. Alkalescent nucleoside was confirmed by the Doskochilova solvent system. The bio-fabricated ZnONPs were characterized by using Fourier transform infrared (FTIR), X-ray diffraction (XRD), and transmission electron microscopy (TEM) analyses. The XRD spectrum and the TEM images confirmed the crystallinity and the spherical shape of the ZnONPs with an average size of 22 nm. FTIR analysis showed the presence of functional groups, which confirmed the bio-fabrication of ZnONPs from alkalescent nucleoside ANO3. In-vitro studies showed that 75 μg/mL of ZnONPs had a strong inhibitory zone (28.39 mm) against the Magnaporthe grisea and significantly suppressed the spore germination. SEM and TEM observations respectively revealed that ZnONPs caused breakage in hyphae and could damage the cells of M. grisea. Greenhouse experiments revealed that the foliar spray of ZnONPs could control the rice blast disease by 98%. Results also revealed that ZnONPs had positive effects on the growth of the rice plant. The present study suggested that ZnONPs could be fabricated from microbe-derived nucleoside antibiotics without facing the problems of metal toxicity and antimicrobial action, thus overcoming the problem of pathogen resistance. This could be a potent biocontrol agent in rice blast disease management. [ABSTRACT FROM AUTHOR]

Plant residue is an important carbon (C) source for soil communities that motivates underground C cycling. However, the effects of plant residue quantity on the structure of the soil micro‐food web and the transformation of exogenous C within the micro‐food web after increasing organic input are not known. Thus, a microcosm experiment was carried out to investigate the responses of soil micro‐food web (including microorganisms and nematodes) to different amounts of 13C‐labelled maize residue addition treatments [without residue addition, 1/3 (1/3R), 2/3 (2/3R) and total residue addition (R)]. The abundances of residue 13C in CO2 (13CO2), soil organic C (SO13C), microorganisms (13C‐microorganisms) and nematodes (13C‐nematodes) were determined after 1, 7, 35 and 84 days. Increasing organic input changed the micro‐food web composition and increased the amount of 13C‐bacteria, 13C‐fungi and 13C‐fungivores but not 13C‐bacterivores. The result of the 13C‐based network showed that bacterivores were positively correlated with omnivores‐predators at the early stage after increasing organic input, while fungivores were at the late stage. Greater 13CO2/SO13C but lower SO13C/total 13C input ratios were found in the R than in the 1/3R treatment at the early stage. At the late stage, the R treatment decreased both 13CO2/total 13C input and 13CO2/SO13C ratios. We concluded that increasing organic input strengthened the trophic interactions between microorganisms and nematodes. The transformation of exogenous C from bacteria to bacterivores might accelerate the turnover of soil C pool, however, the C flow from fungi to fungivores and then to omnivores‐predators could contribute to the exogenous C sequestration in soil. [ABSTRACT FROM AUTHOR]

BACKGROUND: Plant growth‐promoting rhizobacteria may significantly impact the soil microbial community and the growth of plant roots and have critical roles in soil ecosystem functioning. However, the interactions between rhizobacteria and plants are extremely complicated and remain understudied. RESULTS: In this study, a Bacillus strain was isolated from a long‐term maize colonization soil and identified as Bacillus aryabhattai strain LAD. Laboratory tests showed that B. aryabhattai LAD had phosphate‐solubilizing and nitrogen‐fixing functions that benefit plant growth. The effects of LAD cultures on the root system development of corn seedlings and the structure of rhizosphere bacterial communities were studied. The most significant stimulations of LAD culture on plant growth were observed at a cell density of 102 CFU mL−1. Treatment with LAD culture in hydroponics caused an increase of 107%, 197%, and 25% in the shoot length, total root length, and main root thickness respectively. The LAD treatment also significantly affected the rhizosphere microbial abundance and community structure. The rhizobacterial abundance and species richness in the corn seedlings treated with LAD culture were significantly lower than those in the control group. However, the LAD‐treated samples had higher relative abundances of plant growth‐promoting rhizobacteria like Bacillus and Burkholderia than the control samples did, suggesting that LAD treatment may facilitate the mutualistic relation between the rhizosphere microbiome and the plant. CONCLUSION: These results collectively demonstrated that LAD is capable of shaping the rhizosphere microbial community structure and functions as a plant growth‐promoting agent, which makes it a strong candidate for application as bio‐fertilizer in agricultural systems. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]