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The numbers of shared genes between a given plasmid and different chromosomes varied greatly.
As previously pointed out, PAGs may derive from homologous recombination or homology-facilitated illegitimate recombination between a given plasmid and/or other informative molecules, that is phages, chromosomes or other plasmids.
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Two independent yeast strains carrying a given plasmid were monitored; the plasmid copy number in replicate strains was averaged as shown in Table S2.
The transcriptional activity of a given reporter plasmid is listed relative to its respective promoter-less control vector.
A 6.2 kb genomic fragment of the 3' untranslated region of the OGR1 locus was subcloned into plasmid #182 to give plasmid #189.
To calculate the fitness effects of StrR mutations or the plasmid in a given genetic background, we took the difference in fitness (Δ w) between the same strain with and without K43N, K88R or the plasmid.
The plasmids from all the white clones were screened for deletions by PCR and all those with undeleted plasmids from a given transfection were sequenced.
Applying this model on the plasmid control data before the natural samples further gave empirical assessment of false positive rates in the data for a given error rate.
Given that plasmid conjugation machineries are likely the ancestors to many of these modified T4SSs, the role of plasmids in the acquirement of virulence is an exciting area for research, particularly for systems wherein plasmids are plastic, such as rickettsiae.
After a digestion step with PmlI and AscI, the PCR fragment was cloned into the PmlI, AscI digested pbTy plasmid, giving the pbTybceABΔloop plasmid.
Recombinant adenovirus vectors were generated in PER.C6™ cells by homologous recombination between an Adapter plasmid (pAdapt) and the E1 deleted Ad 5 DNA plasmid as described elsewhere [ 34].
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