Similar protocols

Pipeline publication

[…] ate, 1 × Buffer Tango™ and 10 U each of endonucleases RsaI and HhaI (Fermentas, France), as previously described []. DNA fragments were separated on 2% agarose gels stained with ethidium bromide with a 50-bp DNA ladder marker (Fermentas). Isolates showing the same restriction pattern with the two endonucleases were considered to be similar., Both strands of 16S rDNA amplified from isolates representative of each ARDRA profile were sequenced at Biofidal-DTAMB (FR Bio-Environment and Health, Lyon, France). Sequences were manually curated and assembled from forward and reverse primer-generated sequences. Curated sequences were then compared to available bacterial sequences in GenBank using the BLASTn program in the National Center for Biotechnology Information (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The Ribosomal Database Project II Chimera Check was used (http://wdcm.nig.ac.jp/RDP/html/analyses.html) to discard any chimeric sequences., Phylogenetic analyses were performed on a set of Pantoea sequences. Sequences of 16S rRNA genes from Pantoea isolates from mosquitoes were compared to all available sequences of Pantoea retrieved from GenBank that originated from other insect species and environments. Sequences were aligned using ClustalW then corrected manually using Bioedit software []. The resulting alignment was used to construct a maximum-likelihood tree using Seaview v.4.2.12. (http://pbil.univ-lyon1.fr/software/seaview.html). The tree topology was tested by bootstrap analysis with 1,000 resamplings., Undigested genomes of Pantoea isolates were analysed by PFGE according to published protocols with some modifications [,]. Briefly, isolates were grown in 10 ml of LBm liquid medium for 18 h at 30°C. Cell cultures were centrifuged at 5,000 g for 20 min at 4°C. The pellet was resuspended in 1 ml of 1 × Tris-EDTA buffer to obtain an optical density between 1.8 and 2.0. Cell suspensions (0.5 ml) were mixed volume to volume with 1.6% low melting point agarose (Biorad) and the mixture was distributed per 0.1 ml in the plug molds (Biorad) and cooled at 4° […]

Pipeline specifications

Software tools BLASTN, Clustal W, BioEdit, SeaView