Both Lukehart's group and a team at the Centers for Disease Control and Prevention CDCC) in Atlanta have already come up with schemes to track the strains based on the TPR genes, which vary from one strain to another.
The clonal genealogy of the strains based on the whole genome was estimated using a model-based approach to determine bacterial microevolution implemented in ClonalFrame [ 48].
The classical metabolic engineering procedures of constructing and screening strains, based on the collective wisdom of experience, are often complemented with one or more of the new tools to improve and/or fine-tune strain design.
The relationship of the reference strain and the test strains based on the presence and divergence of genes was determined with Bayesian-based algorithms implemented through MR BAYES 3.1 [ 30], as previously described [ 31].
Results are used to develop a means of predicting peak residual strains based on the final plate dimensions - a useful quality control measure.
The shear locking is eliminated by approximating the curvature changes and transverse shear strains based on the solution of the Timoshenko beam equations.
Near full-length 16S rRNA gene sequencing was used to identify unknown bacteriocin producing LAB strains based on the method of Abnous et al. ([2009]).
Through the alignment of homologous nucleotide sequence of known bacteria, phylogenetic relationships could be inferred, and the phylogenetic position of the strain and related strains based on the 16S rDNA sequence is shown in Fig. 1.
These cyathane derivatives are termed "hericenones" and "erinacines". The levels of these compounds can vary substantially between strains, based on the measurements our team has conducted.
ClonalFrame version 1.1 [54] was used for grouping strains based on the sequences of individual genes.
Clustering of strains based on the resulting digital IS-profiles showed a very high correlation to MLST and AFLP based clustering.
