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Pipeline publication

[…] cerevisiae on the surface of YPD agar medium, and plates were then incubated at 30°C or room temperature for up to 14 days, SEM was used to examine strains grown on YPD or MYM agar for up to 14 days. Samples were prepared and visualized using a TEMSCAN LSU scanning electron microscopy as described previously (). To monitor the rate of exploratory growth (), an Olympus SZX12 Sterioscope and CoolSNAP HQ photometric camera were used to capture 70 frames of growth over the course of 17 hr., rpoB () was amplified from each of the 19 exploration-competent wild isolates using primers RpoBPF and RpoBPR (), before being sequenced using RpoBF1 and RpoBR1 (). Trimmed rpoB sequences were aligned using Mafft version 7.2.6.6. A maximum likelihood tree was built using RAxML version 8.2.4 (), using a GTRGAMMA model of nucleotide substitution, with 500 bootstrap replicates to infer support values of nodes. Outputs were visualized using FigTree., Overnight cultures of S. venezuelae were spotted onto rectangular plates containing YPD agar (OmniTray: Nunc International) using a 384-pin replicator. Each strain of a S. cerevisiae BY4741 haploid deletion library was inoculated beside an individual S. venezuelae colony using a 384-pin replicator. Plates were grown for five days at 30°C and screened for an absence of S. venezuelae exploratory growth. Yeast mutants unable to stimulate S. venezuelae exploratory growth were re-tested on individual YPD agar plates. For C. albicans deletion screens, C. albicans GRACE collection tetracycline repressible deletion mutants () were inoculated beside S. venezuelae on YPD agar plates. Mutants […]

Pipeline specifications

Software tools MAFFT, RAxML, FigTree