DeepTetrad: high-throughput image analysis of meiotic tetrads by deep learning in Arabidopsis thaliana.

Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be measured by observing the inheritance of linked transgenes expressing different colors of fluorescent protein in Arabidopsis pollen tetrads. Here we establish DeepTetrad, a deep learning-based image recognition package for pollen tetrad analysis that enables high-throughput measurements of crossover frequency and interference in individual plants. DeepTetrad will accelerate the genetic dissection of mechanisms that control meiotic recombination.

Coumarins reduce biofilm formation and the virulence of Escherichia coli O157:H7.

E. coli O157:H7 is the most common cause of hemorrhagic colitis, and no effective therapy exists for E. coli O157:H7 infection. Biofilm formation is closely related to E. coli O157:H7 infection and constitutes a mechanism of antimicrobial resistance. Hence, the antibiofilm or antivirulence approach provides an alternative to antibiotic strategies. Coumarin and its derivatives have a broad range of biological effects, and in this study, the antibiofilm activities of nine coumarins were investigated against E. coli O157:H7. Coumarin or umbelliferone at 50µg/ml was found to inhibit biofilm E. coli O157:H7 formation by more than 80% without affecting bacterial growth. Transcriptional analysis showed that coumarins repressed curli genes and motility genes in E. coli O157:H7, and these findings were in-line with observed reductions in fimbriae production, swarming motility, and biofilm formation. In addition, esculetin repressed Shiga-like toxin gene stx2 in E. coli O157:H7 and attenuated its virulence in vivo in the nematode Caenorhabditis elegans. These findings show that coumarins have potential use in antivirulence strategies against persistent E. coli O157:H7 infection.

Diverse plant extracts and trans-resveratrol inhibit biofilm formation and swarming of Escherichia coli O157:H7.

Infection with enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a worldwide problem. Of the 498 plant extracts screened against EHEC, 16 inhibited the formation of biofilm of EHEC by >85% without inhibiting the growth of planktonic cells, and 14 plant extracts reduced the swarming motility of EHEC. The most active extract, Carex dimorpholepis, decreased swimming and swarming motilities and curli formation. Transcriptional analyses showed that the extract of C. dimorpholepis repressed curli genes, various motility genes, and AI-2 quorum sensing genes, which was corroborated by reduction in the production of fimbria, motility, and biofilm by EHEC. Trans-resveratrol at 10 µg ml(-1) in the extract of C. dimorpholepis was found to be a new anti-biofilm compound against EHEC, but importantly, the extract of C. dimorpholepis and trans-resveratrol did not inhibit the fomation of biofilm in four commensal E. coli strains. Furthermore, the extract of C. dimorpholepis decreased the adhesion of EHEC cells to human epithelial cells without affecting the viability of these cells.

Inhibition of Pseudomonas aeruginosa and Escherichia coli O157:H7 biofilm formation by plant metabolite ε-viniferin.

Pathogenic biofilms are associated with persistent infection due to their high resistances to diverse antibiotics. Pseudomonas aeruginosa infects plants, animals, and humans and is a major cause of nosocomial diseases in patients with cystic fibrosis. In the present study, the antibiofilm abilities of 522 plant extracts against P. aeruginosa PA14 were examined. Three Carex plant extracts at a concentration of 200 µg/mL inhibited P. aeruginosa biofilm formation by >80% without affecting planktonic cell growth. In the most active extract of Carex pumila , resveratrol dimer ε-viniferin was one of the main antibiofilm compounds against P. aeruginosa. Interestingly, ε-viniferin at 10 µg/mL inhibited biofilm formation of enterohemorrhagic Escherichia coli O157:H7 by 98%. Although Carex extracts and trans-resveratrol are known to possess antimicrobial activity, this study is the first to report that C. pumila extract and ε-viniferin have antibiofilm activity against P. aeruginosa and E. coli O157:H7.

Anti-biofilm activities of quercetin and tannic acid against Staphylococcus aureus.

Staphylococcus aureus is a leading cause of nosocomial infections because of its resistance to diverse antibiotics. The formation of a biofilm is one of the mechanisms of drug resistance in S. aureus. The anti-biofilm abilities of 498 plant extracts against S. aureus were examined. Seventy-two plant extracts belonging to 59 genera and 38 families were found to significantly inhibit the formation of biofilms of S. aureus without affecting the growth of planktonic cells. The most active extract, from Alnus japonica, inhibited the formation of biofilms by three S. aureus strains by >70% at 20 µg ml(-1). Transcriptional analyses showed that extract of A. japonica repressed the intercellular adhesion genes icaA and icaD most markedly. Quercetin and tannic acid are major anti-biofilm compounds in the extract of A. japonica. Additionally, the extract of A. japonica and its component compound quercetin, reduced hemolysis by S. aureus. This phenomenon was not observed in the treatment with tannic acid. This study suggests that various plant extracts, such as quercetin and tannic acid, could be used to inhibit the formation of recalcitrant biofilms of S. aureus.