The Sombor index and coindex of two-trees

The Sombor index of a graph $G$, introduced by Ivan Gutman, is defined as the sum of the weights $\sqrt{d_G(u)^2+d_G(v)^2}$ of all edges $uv$ of $G$, where $d_G(u)$ denotes the degree of vertex $u$ in $G$. The Sombor coindex was recently defined as $\overline{SO}(G) = \sum_{uv\notin E(G)}\sqrt{d_G(u)^2+d_G(v)^2}$. As a new vertex-degree-based topological index, the Sombor index is important because it has been proved to predict certain physicochemical properties. Two-trees are very important structures in complex networks. In this paper, the maximum and second maximum Sombor index, the minimum and second minimum Sombor coindex of two-trees and the extremal two-trees are determined, respectively. Besides, some problems are proposed for further research

Acetate and auto-inducing peptide are independent triggers of quorum sensing in Lactobacillus plantarum

The synthesis of plantaricin in Lactobacillus plantarum is regulated by quorum sensing. However, the nature of the extra-cytoplasmic (EC) sensing domain of the histidine kinase (PlnB1) and the ability to recognize the auto-inducing peptide PlnA1 is not known. We demonstrate the key motif Ile-Ser-Met-Leu of auto-inducing peptide PlnA1 binds to the hydrophobic region Phe-Ala-Ser-Gln-Phe of EC loop 2 of PlnB1 via hydrophobic interactions and hydrogen bonding. Moreover, we identify a new inducer, acetate, that regulates the synthesis of plantaricin by binding to a positively charged region (Arg-Arg-Tyr-Ser-His-Lys) in loop 4 of PlnB1 via electrostatic interaction. The side chain of Phe143 on loop 4 determined the specificity and affinity of PlnB1 to recognize acetate. PlnA1 activates quorum sensing in log phase growth and acetate in stationary phase to maintain the synthesis of plantaricin under conditions of reduced growth. Acetate activation of PlnB was also evident in four types of PlnB present in different Lb. plantarum strains. Finally, we proposed a model to explain the developmental regulation of plantaricin synthesis by PlnA and acetate. These results have potential applications in improving food fermentation and bacteriocin production

Genome Mining, Heterologous Expression, Antibacterial and Antioxidant Activities of Lipoamides and Amicoumacins from Compost-Associated Bacillus subtilis fmb60

Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities, was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1–3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated

Identification and characterization of an Aeromonas hydrophila oligopeptidase gene pepF negatively related to biofilm formation

Bacterial biofilms are involved in adapting to the complex environment and responsible for bacterial persistent infection. The formation of biofilm is a highly complex process during which multifarious genes work together regularly. In this study, we screened the EZ-Tn5 transposon mutant library aiming at identifying the genes involved in biofilm formation of Aeromonas hydrophila. A total of 24 biofilm-associated genes were identified, and the majority of them encoded proteins related to cell structure, transcription and translation, gene regulation, growth and metabolism. The mutant strain TM90, in which a gene encoding oligopeptidase F, pepF, was disturbed, showed significant upregulation of biofilm formation as compared to the parental strain. Meanwhile, the colony phenotype of TM90 became smaller, more transparent and splendent. The adhesive ability of TM90 to HEp-2 cell was significantly increased compared with the parental strain. Fifty percent lethal dose (LD50) determinations in zebrafish demonstrated that the enhanced-biofilm mutant TM90 was highly attenuated relative to the wild-type strain. In conclusion, the pepF gene is first demonstrated to be a negative factor on biofilm formation and involved in pathogenicity of A. hydrophila

Catecholamine-stimulated Growth of Aeromonas hydrophila Requires the TonB2 Energy Transduction System but is Independent of the Amonabactin Siderophore

The growth-stimulating effects of catecholamine stress hormones have been demonstrated in many pathogens. However, catecholamine-induced growth and its underlying mechanisms remain poorly understood in Aeromonas hydrophila. The present study sought to demonstrate that norepinephrine (NE), epinephrine (Epi), dopamine (Dopa) and L-dopa stimulate the growth of A. hydrophila in iron-restricted media containing serum. NE exhibited the strongest growth stimulation, which could be blocked by adrenergic antagonists. Furthermore, it was demonstrated that NE could sequester iron from transferrin, thereby providing a more accessible iron source for utilization by A. hydrophila. The deletion of the amoA gene associated with amonabactin synthesis revealed that the amonabactin siderophore is not required for NE-stimulated growth. However, the deletion of the TonB2 energy transduction system resulted in the loss of growth promotion by NE, indicating that a specific TonB-dependent outer membrane receptor might be involved in the transport of iron from transferrin. Collectively, our data show that catecholamine sensing promotes the growth of A. hydrophila in a manner that is dependent on the TonB2 energy transduction system

Ultrasound-assisted fermentation of Porphyra yezoensis sauce at different growth stages using Lactiplantibacillus plantarum: Metabolic response and biological activity

This study first employed ultrasonic-assisted fermentation of seaweed foot material with Lactiplantibacillus plantarum to produce Porphyra yezoensis sauce. The aim was to examine L. plantarum's growth and metabolism of nutritional components at different growth stages under low- (133.99 W/L) and high-ultrasonic power densities (169.17 W/L). After 24-h fermentation, L. plantarum exhibited a 21.32 % increase in the sonicated P. yezoensis sauce at 133.99 W/L and the logarithmic growth phase compared to that at 169.17 W/L. In addition, compared to the non-sonicated sauce, total phenolic and flavonoid contents increased by around 58 % and 27 % in sonicated sauce at 133.99 W/L, reaching 92.38 mg GEA/g DW and 111.08 mg RE/g DW, respectively. Principal Component Analysis (PCA) of the evaluation criteria for different fermentation stages under 133.99 W/L power ultrasonication revealed that the P. yezoensis sauce generated more phenolic compounds and exhibited stronger antioxidant capabilities in the sonicated sample at the logarithmic phase of L. plantarum. Compared to the traditional treated P. yezoensis sauce, the content of free amino acids was significantly increased in sonicated sauce, especially for logarithmic phase. Finally, GC-IMS analysis demonstrated that the ultrasonication at logarithmic phase released more volatile compounds compared to the non-sonicated sauce. This led to a reduction in the fishy odour of the Porphyra yezoensis sauce and an improved release of favourable flavour compounds