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Pipeline publication

[…] ons of samples from different culture conditions were added to the medium, which was placed in an incubator at 28 °C. After 24 hours of culture, transparent circles were observed if AHL was degraded and violacein synthesis was inhibited. The area of transparent circle was calculated and the mean value of three repeated experiment was used., Protein domains were analyzed by SMART software (http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1) for online analysis. The suf and momL sequences of the different strains were analyzed by BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Annotation and bioinformatic analysis were performed on the flanking genes of momL by genome sequencing and EMBOSS (The European Molecular Biology Open Software Suite) (http://emboss.open-bio.org/). DNAMAN software was used to compare the three copies of the OxyR protein. Primers for real-time fluorescent quantitative PCR were designed using Primer Premier 5., The two types of bacteria were cultured in LB medium separately, and cells were collected by centrifugation when the OD600 reached 0.8. The two types of bacteria were mixed and cultured in 10% tryptic soy broth (TSB) medium with 2 mM H2O2 for 6 hours. The bacterial co-culture was serially diluted. At each concentration, dilutions were spread onto two LB plates, one of which contained 25 µg/mL Km. The survival of Pcc was the difference between the bacterial counts of the two LB plates (NumbersLB − NumbersLB+Km)., Pcc and M. olearia Th120 were cultured in LB and MA media, separately until the OD600 reached 0.8. Cultures of the two bacteria were centrifuged, and the two typ […]

Pipeline specifications

Software tools EMBOSS, DNAMAN, Primer Premier