Journal: Biophysical Journal

Article Title: Multiscale Spatial Organization of RNA Polymerase in Escherichia coli

doi: 10.1016/j.bpj.2013.05.048

Figure Lengend Snippet: Super-resolution map of RNAP distribution in E. coli. E. coli strain KF26, in which all RNAP β′ subunits are tagged with PAmCherry1, was grown at 32°C in (A) LB (a rich media) or (B) M9 (a minimal media) to OD600 = 0.4, fixed, and imaged using PALM. Numbers indicate independent molecular localizations per cell. Each panel contains several different images demarcated by gray lines (bars: 1 μm).

Article Snippet: For detection of PAmCherry1 (mouse monoclonal; Clontech 632543, Clontech, Saint-Germain-en-Laye, France), membranes were blocked in TBST + 3% low-fat milk, and incubated with 3 mL 1:1000 primary antibody in TBST.

Techniques:

Journal: Biophysical Journal

Article Title: Multiscale Spatial Organization of RNA Polymerase in Escherichia coli

doi: 10.1016/j.bpj.2013.05.048

Figure Lengend Snippet: RNAP molecules are found in bands. E. coli cells expressing β′-PAmCherry1 were grown in LB (A and B) or M9 media (C and D), fixed, and imaged using PALM and bright field microscopy. (A) Three views of four fields are shown (largest images – PALM; top-left image of pair – bright field image; top-right image of pair – reconstruction of a conventional fluorescence image using super-resolution coordinate lists obtained by PALM) above the corresponding longitudinal RNAP localization densities (determined using PALM, solid black line) and intensity profiles (determined using bright field image, dashed gray line) smoothed using a Savitzky-Golay filter. Fields i–iv include cells of different length (bar: 500 nm). (B) Number of bands per cell as a function of cell length. Cells lacking a septum are shown in black; cells possessing initiating or fully formed septa are shown in blue and orange, respectively. (C and D) Analysis as in A and B for cells grown in minimal medium.

Article Snippet: For detection of PAmCherry1 (mouse monoclonal; Clontech 632543, Clontech, Saint-Germain-en-Laye, France), membranes were blocked in TBST + 3% low-fat milk, and incubated with 3 mL 1:1000 primary antibody in TBST.

Techniques: Expressing, Microscopy, Fluorescence

Journal: Biophysical Journal

Article Title: Multiscale Spatial Organization of RNA Polymerase in Escherichia coli

doi: 10.1016/j.bpj.2013.05.048

Figure Lengend Snippet: Clustering analysis. E. coli expressing free PAmCherry1 (i) or β′-PAmCherry1 (ii, iii) were grown in rich LB (i, iii) or minimal M9 media (ii), fixed, and imaged using PALM, and the resulting localization lists subjected to DBSCAN cluster analysis. (A) PALM images are shown above localizations plotted as crosses (crosses in one cluster share the same randomly chosen color). Bars: 500 nm. (B) Sizes of clusters observed in cells in panel A. For ease of comparison, the solid gray line shows the frequency distribution for free PAmCherry1 (i), normalized to the maximum frequency in each panel. Blue, green, and yellow backgrounds identify regions containing clustered molecules.

Article Snippet: For detection of PAmCherry1 (mouse monoclonal; Clontech 632543, Clontech, Saint-Germain-en-Laye, France), membranes were blocked in TBST + 3% low-fat milk, and incubated with 3 mL 1:1000 primary antibody in TBST.

Techniques: Expressing

Journal: eLife

Article Title: Sox9+ messenger cells orchestrate large-scale skeletal regeneration in the mammalian rib

doi: 10.7554/eLife.40715

Figure Lengend Snippet:

Article Snippet: Slides were blocked in 20% serum for 1 hr and then incubated with the primary antibodies overnight at 4°C (anti-pHH3, Millipore: 06–570, 1:200; anti-mCherry which also detects tdTomato, Novus Biological: NBP2-25158SS, 1:200; anti-Col1, Abcam: ab34710, 1:250; anti-Col2, Southern Biotech: 1320–01, 1:200).

Techniques: