A genome-wide association study reveals that epistasis underlies the pathogenicity of Pectobacterium.

Pectobacterium spp. are important bacterial pathogens that cause soft rot symptoms in various crops. However, their mechanism of pathogenicity requires clarity to help control their infections. Here, genome-wide association studies (GWAS) were conducted by integrating genomic data and measurements of two phenotypes (virulence and cellulase activity) for 120 various Pectobacterium strains in order to identify the genetic basis of their pathogenicity. An artificial intelligence-based software program was developed to automatically measure lesion areas on Chinese cabbage, thereby facilitating accurate and rapid data collection for virulence phenotypes for use in GWAS analysis. The analysis discovered 428 and 158 loci significantly associated with Pectobacterium virulence (lesion area) and cellulase activity, respectively. In addition, 1,229 and 586 epistasis loci pairs were identified for the virulence and cellulase activity phenotypes, respectively. Among them, the AraC transcriptional regulator exerted epistasis effects with another three nutrient transport-related genes in pairs contributing to the virulence phenotype, and their epistatic effects were experimentally confirmed for one pair with knockout mutants of each single gene and double gene. This study consequently provides valuable insights into the genetic mechanism underlying Pectobacterium spp. pathogenicity. IMPORTANCE Plant diseases and pests are responsible for the loss of up to 40% of food crops, and annual economic losses caused by plant diseases reach more than $220 billion. Fighting against plant diseases requires an understanding of the pathogenic mechanisms of pathogens. This study adopted an advanced approach using population genomics integrated with virulence-related phenotype data to investigate the genetic basis of Pectobacterium spp., which causes serious crop losses worldwide. An automated software program based on artificial intelligence was developed to measure the virulence phenotype (lesion area), which greatly facilitated this research. The analysis predicted key genomic loci that were highly associated with virulence phenotypes, exhibited epistasis effects, and were further confirmed as critical for virulence with mutant gene deletion experiments. The present study provides new insights into the genetic determinants associated with Pectobacterium pathogenicity and provides a valuable new software resource that can be adapted to improve plant infection measurements.

Hydrodynamic cavitation-enhanced photocatalytic activity of P-doped TiO2 for degradation of ciprofloxacin: Synergetic effect and mechanism.

Hybrid methods with an enhanced oxidation capacity have been proposed for the removal of organic contaminants based on combining hydrodynamic cavitation (HC) with advanced oxidation processes (AOPs). In this study, we utilize the synergetic effect between photocatalytic processes and HC to strengthen ciprofloxacin (CIP) degradation by P-doped TiO2 catalysts. In comparison to a degradation ratio of 20.37 % in HC and 55.7 % in P-TiO2-based photocatalytic processes alone, the CIP degradation ratio reached as high as 90.63 % in HC-assisted photocatalytic processes with the optimal experimental parameters. The mechanic microjets treatment originated from HC make P-TiO2 nano photocatalysts with significantly increased surface area, smaller particle sizes, cleaner surface and improved dispersion, which were found using SEM, TEM, and BET analysis. Possible degradation mechanisms and reaction pathways of CIP during hybrid HC + photocatalytic processes were explored by coupling free radical capture experiments and liquid chromatography-mass spectrometry . This hybrid HC + photocatalytic technique has a potential application in the treatment of antibiotic sewage at the industrial level.

Microfluidic-templating alginate microgels crosslinked by different metal ions as engineered microenvironment to regulate stem cell behavior for osteogenesis.

Cell microenvironment is a collection of dynamic biochemical and biophysical cues which functions as the key factor in determining cell behavior. Encapsulating single cell into micrometer-scale hydrogels which mimics the cell microenvironment can be used for single cell analysis, cell therapies, and tissue engineering. Here, we developed a microfluidics-based platform to engineer the niche environment at single cell level using alginate microgels crosslinked by different metal ions to regulate stem cell behavior for bone regeneration. Specifically, we revealed that Ca2+ in the engineered microenvironment promoted osteogenic differentiation of encapsulated stem cells and substantially accelerated the matrix mineralization compared to Sr2+in vitro. However, the superior osteoinductive capacity of Ca2+ compared with Sr2+ led to comparable bone healing in a rat bone defect model. This attributed to Sr2+ in microgels to inhibit the osteoclast activity and bone resorption after implantation. In summary, the present study demonstrates metal ions as a critical factor in the environmental cues to affect cell behavior and influence the efficacy of stem cell-based therapy in tissue regeneration, and provides new insights to engineer an expecting microenvironment for regenerative medicine.