Journal: mBio

Article Title: The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes

doi: 10.1128/mBio.01226-19

Figure Lengend Snippet: The BPS rate pattern of MMR-defective strains. The BPS data from 10 experiments performed with MMR-defective strains were collected into 100-kb bins starting at the origin of replication shown on the left (bin 1) and continuing clockwise around the chromosome back to the origin shown on the right (bin 46). (A) Bars represent the mean BPS rate in each bin; error bars represent 95% CL of the mean. The gray line represents the Daubechies wavelet transform of the binned data. The chromosomal macrodomains (MDs) are indicated at the top of the plot as follows: green, Ori MD; blue, right and left MD; red, Ter MD. (B) Plot of the wavelet coherence between the binned BPS data from the MMR-defective strains taken in the clockwise and counterclockwise directions around the chromosome. The colors indicate the magnitude-squared coherence, a measure of the correlation between the data sets, according to the scale on the right. The dotted line gives the “cone of influence” within which the results are free of artifactual edge effects. Arrows indicate the phase lag between the two data sets; arrows pointing right indicate in phase, arrows pointing left indicate 180° out of phase, and arrows pointing in other directions indicate the various degrees between.

Article Snippet: In addition, the MatLab wavelet coherence plot indicates, as a dashed curve, the “cone of influence” within which results are free of artifactual edge effects ( ).

Techniques:

Journal: mBio

Article Title: The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes

doi: 10.1128/mBio.01226-19

Figure Lengend Snippet: Comparison of the pattern of BPS rates to transcription levels. (A) The Daubechies wavelet transform of the binned reads from RNA-Seq samples taken during lag, log, and stationary-growth phases of Δ mutL mutant strain PFM144. The data used for the wavelet transforms represent means of results from three biological replicates. Arrows indicate the positions of the rRNA operons, but the reads from the ribosomal genes in those operons were not included in the plot (see Materials and Methods). (B) Plot of the wavelet coherence between the BPS data from the MMR-defective strains and the mean binned reads from RNA-Seq samples taken during lag, log, and stationary-growth phases of the Δ mutL mutant strain (see the legend to Fig. 1B for further explanation of the coherence plot.).

Article Snippet: In addition, the MatLab wavelet coherence plot indicates, as a dashed curve, the “cone of influence” within which results are free of artifactual edge effects ( ).

Techniques: Comparison, RNA Sequencing, Mutagenesis

Journal: mBio

Article Title: The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes

doi: 10.1128/mBio.01226-19

Figure Lengend Snippet: The effect on the BPS rate pattern of relocating OriC. (A) Bars represent the BPS rate in each bin for the Δ oriC oriZ + Δ mutL mutant strain (PFM426), and the pink line represents the Daubechies wavelet transform of the binned data (scale on left axis). The gray line represents the Daubechies wavelet transform of the binned data from the 10 MMR − strains (scale on right axis; adjusted to bring the wavelets together for comparison). (B) Plot of the wavelet coherences between the data from the Δ oriC oriZ + Δ mutL mutant strain and the data from the 10 MMR − strains. (See the legend to Fig. 1 for further explanations of the bar charts and the coherence plots.) The arrow in panel A indicates the position of oriZ + .

Article Snippet: In addition, the MatLab wavelet coherence plot indicates, as a dashed curve, the “cone of influence” within which results are free of artifactual edge effects ( ).

Techniques: Mutagenesis, Comparison

Journal: mBio

Article Title: The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes

doi: 10.1128/mBio.01226-19

Figure Lengend Snippet: The BPS rate pattern of MMR-defective B. subtilis . (A) Bars represent the BPS rate in each bin for the B. subtilis MMR-defective strains; the pink line represents the Daubechies wavelet transform of the binned data (scale on left axis). The gray line represents the Daubechies wavelet transform of the binned data from the 10 E. coli MMR − strains (scale on right axis; adjusted to bring the wavelets together for comparison). (B) Plot of the wavelet coherence between the binned BPS data from the B. subtilis strains taken in the clockwise and counterclockwise directions around the chromosome. (See the legend to Fig. 1 for further explanations of the bar charts and of the coherence plots). Strains: four B. subtilis mutS ::Tn 10 strains with the same mutational phenotype ( Table 3 ) (see also Table S1 in the supplemental material).

Article Snippet: In addition, the MatLab wavelet coherence plot indicates, as a dashed curve, the “cone of influence” within which results are free of artifactual edge effects ( ).

Techniques: Comparison