Journal:

Article Title: Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection

doi: 10.1128/AAC.49.8.3203-3207.2005

Figure Lengend Snippet: Inhibition of E. coli mutant SM101 growth in vitro by acpP-targeting PNA. PNA was added to cell cultures containing 5 × 105 CFU/ml SM101 to a final concentration of 4, 40, or 400 μM as indicated on the graph, with addition of an equal volume of water as a control (0 μM). Cultures were incubated as described in Materials and Methods. Aliquots of each culture were collected at 2 and 4 h, diluted, and plated for viable cell determination. Error bars indicate standard deviations of the results from three experiments (*, P < 0.01 relative to 2 h control; **, P < 0.001 relative to 4-h control [as determined by Student's t test]).

Article Snippet: E. coli strain K-12 was obtained from the American Type Culture Collection (ATCC 29425) and grown at 37°C in nutrient broth.

Techniques: Inhibition, Mutagenesis, In Vitro, Concentration Assay, Incubation

Journal:

Article Title: Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection

doi: 10.1128/AAC.49.8.3203-3207.2005

Figure Lengend Snippet: Inhibition of E. coli wild-type K-12 growth in vitro by acpP-targeting peptide-PNA conjugate. Peptide-PNA conjugate was added to cell cultures containing 5 × 105 CFU/ml E. coli strain K-12 to a final concentration of 0, 4, 40, or 400 μM as indicated on the graph. Cell cultures were grown, and viable cells were determined as described in the legend to Fig. ​Fig.1.1. Error bars indicate standard deviations of the results from two experiments (*, P < 0.001 relative to 2-h control; **, P < 0.005 relative to 4-h control [as determined by Student's t test]).

Article Snippet: E. coli strain K-12 was obtained from the American Type Culture Collection (ATCC 29425) and grown at 37°C in nutrient broth.

Techniques: Inhibition, In Vitro, Concentration Assay

Journal:

Article Title: Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection

doi: 10.1128/AAC.49.8.3203-3207.2005

Figure Lengend Snippet: Survival of K-12-infected mice due to treatment with acpP-targeting peptide-PNA conjugate. Six-week-old BALB/c mice were i.p. infected with 8 × 108 CFU E. coli strain K-12 in 500 μl PBS (LD90). Infected mice were treated with the peptide-PNA conjugate (100 or 500 nmol) 30 min postinfection; comparisons are made to untreated mice. Survival and general health of these animals was monitored every 6 to 12 h through 9 days.

Article Snippet: E. coli strain K-12 was obtained from the American Type Culture Collection (ATCC 29425) and grown at 37°C in nutrient broth.

Techniques: Infection

Journal:

Article Title: Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection

doi: 10.1128/AAC.49.8.3203-3207.2005

Figure Lengend Snippet: Reduction of E. coli K-12 bacteremia in mice following treatment with peptide-PNA conjugate a

Article Snippet: E. coli strain K-12 was obtained from the American Type Culture Collection (ATCC 29425) and grown at 37°C in nutrient broth.

Techniques:

Journal: bioRxiv

Article Title: Labelizer: systematic selection of protein residues for covalent fluorophore labeling

doi: 10.1101/2023.06.12.544586

Figure Lengend Snippet: A) Visualization of the selected parameter scores from the four categories, which are used as default settings in our webserver for the example of PBP from E.coli [ , ]; pdb:1OIB. B) Visualization of the label score on PBP based on default parameters shown in panel A. C) Label score histogram of all residues (gray) and labeled residues (red) in the database. The pale area shows the 95% confidence interval of 400 bootstrapping runs. D) Additional examples of LS values indicated on protein structures for a membrane protein (left, LeuT of in A. aeolicus[ , ], pdb:2A65) and a DNA-binding protein (right, DNA polymerase I of B. stearothermophilus[ , ] with DNA template, pdb:1L3U).

Article Snippet: The coding sequence for the E. coli K12 phoS gene (Genbank coding sequence NC_000913.3 , 3910485 - 3911525 complement, protein accession number NP_418184.1 ), with amino-acid changes (A17C and A197C) corresponding to the rho-PBP fluorescent biosensor variant[ ] was synthesized (Invitrogen GeneArt Gene Synthesis, Thermo Fisher) without its N-terminal signal sequence (25 amino acid N-terminal deletion).

Techniques: Labeling, Binding Assay