Journal: eLife

Article Title: The evolution of a counter-defense mechanism in a virus constrains its host range

doi: 10.7554/eLife.79549

Figure Lengend Snippet:

Article Snippet: Strain, strain background (T2) , T2 , ATCC , Cat# 11303-B2; phML-38 , N/A.

Techniques: Clone Assay, Magnetic Beads, Recombinant, Concentration Assay, Plasmid Preparation, Amplification, Software, Sequencing, DNA Sequencing

Journal: PLoS Biology

Article Title: Individual bacteria in structured environments rely on phenotypic resistance to phage

doi: 10.1371/journal.pbio.3001406

Figure Lengend Snippet: Schematics illustrating T4 epidemics in E . coli in (A) well-mixed microwells and (B) microfluidic devices structured with ephemeral spatial refuges. Corresponding temporal dependence of bacterial population size in (C) the unstructured and (D) the structured environment in the presence (triangles) and absence (circles) of phage T4. Data are the mean and standard error of the mean of at least 4 biological replicates in the unstructured environment and of 200 spatial refuges in biological triplicate in the structured environment. Error bars are hidden behind the corresponding data points in the structured environment measurements due to the large statistical samples. It is noteworthy that similar initial bacterial population sizes were used in the unstructured and structured environments; compare data at t = 0. Dashed lines are guides for the eye. Numerical values for each replica in Fig 1C and 1D are provided in Data B and Data F in , respectively.

Article Snippet: T2 and T4 phages (ATCC-11303-B2 and ATCC-11303-B4, respectively) were purchased from LGC Standards (LGC Standards, Middlesex, United Kingdom).

Techniques:

Journal: PLoS Biology

Article Title: Individual bacteria in structured environments rely on phenotypic resistance to phage

doi: 10.1371/journal.pbio.3001406

Figure Lengend Snippet: (A) Temporal dependence of the bacterial population size with T4 phages continuously injected in the mother machine device from t = 0 onwards at an MOI of 1 (circles), 10 3 (triangles), or 10 5 (squares). This MOI refers to the concentrations of phage and bacteria in the entire device rather than in each individual compartment. Data and error bars are the average and standard error of the mean of 200 single-compartment measurements in biological triplicate. The dashed lines are guides for the eye. Some of the error bars are hidden behind the corresponding data points. **** indicates a p -value ≤ 0.0001. ( B ) Corresponding simulated temporal dependence of the fraction of phage-free refuges up to time t . Data points were obtained via Lattice–Boltzmann simulations, and statistics was collected from over 2,600 simulated phages in a periodic cross-section of the mother machine. The dashed lines are guides for the eye. Numerical values for each replica in Fig 2A and 2B are provided in Data J and Data K in , respectively. MOI, multiplicity of infection.

Article Snippet: T2 and T4 phages (ATCC-11303-B2 and ATCC-11303-B4, respectively) were purchased from LGC Standards (LGC Standards, Middlesex, United Kingdom).

Techniques: Injection, Infection

Journal: PLoS Biology

Article Title: Individual bacteria in structured environments rely on phenotypic resistance to phage

doi: 10.1371/journal.pbio.3001406

Figure Lengend Snippet: Representative temporal dependence of bacterial density per compartment for a bacterium that (A) remains viable but nongrowing as determined by live/dead staining at t = 24 h, (B) duplicates and remains alive together with all its progeny, (C) duplicates but some of its progeny lyses, and (D) filaments upon exposure to T4 phage. Measurements were carried out in 200 channels of the structured mother machine environment in biological triplicate. Dashed lines are guides for the eye. Numerical values are provided in Data P in .

Article Snippet: T2 and T4 phages (ATCC-11303-B2 and ATCC-11303-B4, respectively) were purchased from LGC Standards (LGC Standards, Middlesex, United Kingdom).

Techniques: Staining

Journal: PLoS Biology

Article Title: Individual bacteria in structured environments rely on phenotypic resistance to phage

doi: 10.1371/journal.pbio.3001406

Figure Lengend Snippet: Distributions of GFP levels reporting on the expression of the T4 receptor OmpC before exposure to (A) T4 or (B) T2 phage in E . coli that later lysed (green violin plot) or survived (black violin plot) exposure to phage. Data were obtained in biological triplicate for a total of N = 108, N = 42 bacteria that were killed or survived T4 exposure, respectively, and N = 85, N = 42 bacteria that were killed or survived T2 exposure, respectively. Distributions of GFP levels reporting on the expression of the T2 receptor FadL before exposure to (C) T4 or (D) T2 phage in E . coli that later lysed (green violin plot) or survived (black violin plot) exposure to phage. Data were obtained in biological triplicate for a total of N = 82, N = 31 bacteria that were killed or survived T4 exposure, respectively, and N = 72, N = 35 bacteria that were killed or survived T2 exposure, respectively. (E) Temporal dependence of mean bacterial population size for the parental strain (triangles) and a Δ ompC deletion mutant (circles) upon exposure to T4 phage. Data are the mean and standard error of the mean of 200 single-compartment measurements in biological triplicate. Some of the error bars are hidden behind the corresponding data points. Solid lines are linear regression fitting to the data returning an x-intercept of 10 and 17 h for the parental and Δ ompC strain, respectively. Dashed lines are guides for the eye. (f) Distributions of number of generations before death caused by T4 for the parental (red) and Δ ompC strain (blue boxplot). The bottom and top of the box are the first and third quartiles, the line and plus symbol inside the box are the median and mean, the bottom and top lines outside the box represent the 10th and 90th percentiles, respectively. Data were obtained in biological triplicate. ** indicates a p -value ≤ 0.01, **** indicates a p -value ≤ 0.0001. Numerical values for Fig 5A–5D are provided in Data S in . Numerical values for Fig 5E and 5F are provided in Data V and Data W in . GFP, green fluorescent protein; OmpC, outer membrane protein C.

Article Snippet: T2 and T4 phages (ATCC-11303-B2 and ATCC-11303-B4, respectively) were purchased from LGC Standards (LGC Standards, Middlesex, United Kingdom).

Techniques: Expressing, Mutagenesis