Journal: ImmunoHorizons

Article Title: The miR-183/96/182 Cluster Regulates the Functions of Corneal Resident Macrophages

doi: 10.4049/immunohorizons.2000091

Figure Lengend Snippet: ( A–C ) qRT-PCR analysis of miR-183/96/182 expression in corneal ResMϕ in response to a 6-h treatment of P. aeruginosa (MOI = 5) or LPS (100 ng/ml). Relative expression levels (Rel exp) were normalized to no-treatment control (NTC). n = 3 per group. * p < 0.05, ** p < 0.01. ( D ) Sequencing alignment of miR-183, miR-96, or miR-182 with their predicted target sites in the 3′ UTR of mouse TLR4. Gray-shaded residues represent the seed sequences of miRNAs and corresponding predicted target sequences. ( E ) qRT-PCR of TLR4 in FACS-sorted corneal ResMϕ (CD45 + CD11b + F4/80 + ). Rel exp is normalized to wt control mice. *** p < 0.001.

Article Snippet: The cornea of the left eye was wounded; 5.0 × 10 6 CFU P. aeruginosa (strain 19660; American Type Culture Collection [ATCC], Manassas, VA) in a 5-μl vol was topically delivered.

Techniques: Quantitative RT-PCR, Expressing, Control, Sequencing

Journal: ImmunoHorizons

Article Title: The miR-183/96/182 Cluster Regulates the Functions of Corneal Resident Macrophages

doi: 10.4049/immunohorizons.2000091

Figure Lengend Snippet: Corneal stromal flatmount of young adult (8–12 wk old) miR-183/96/182 ko and age-matched wt contro( n = 3 per genotype) at 3 ( A and C ) and 6 hpi ( B and D ) in comparison with naive mouse cornea ( n = 7 per genotype) ( E ). * p < 0.05, *** p < 0.001 in comparison of ko versus wt. # p < 0.05, ## p < 0.01 in comparison with infected (E a ) or contralateral eyes (E b ) of P. aeruginosa-infected mice versus the ones of naive mice. ‡‡ p < 0.01 in comparison with the numbers at 3 versus 6 hpi in ko (above the curves) and wt mice (below the curves).

Article Snippet: The cornea of the left eye was wounded; 5.0 × 10 6 CFU P. aeruginosa (strain 19660; American Type Culture Collection [ATCC], Manassas, VA) in a 5-μl vol was topically delivered.

Techniques: Comparison, Infection

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: The fluorescence of recombinant YM4 cells containing the P rhlA - gfp cassette and P BAD - gfp cassette cultivated in LB medium and rhamnolipid fermentation medium without the addition of any inducer.

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Fluorescence, Recombinant

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: Fermentation performance of strain YM4 and recombinant YM4 cells containing the P rhlA - irrE cassette in batch fermentation. ( a ) The growth of strains; ( b ) the rhamnolipid production of strains. All strains were cultivated in rhamnolipid fermentation medium. The error bars represent standard deviation values of three independent experiments ( n = 3).

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Recombinant, Standard Deviation

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: The variation of kinetic parameters (µ, q p ) of strain XY01 and YM4. ( a ) The specific growth rate (µ, h −1 ); ( b ) the specific rhamnolipid production rate (q p , h −1 ).

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques:

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: Response of cells to stress environment. The growth phenotypes of strain XY01 and YM4 were evaluated on LB agar plates supplemented with 10 g/L or 20 g/L rhamnolipids and with pH adjusted to 7.0, 7.5, and 8.0. All plates were photographed after 12 h incubation at 37 °C.

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Incubation

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: HPLC-ELSD profiles of rhamnolipids produced from strain YM4 and XY01. Rhamnolipids standard (R90, Lot number: A79125126058) was obtained from AGAE Technologies (Corvallis, OR, USA).

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Produced

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: Structural composition of rhamnolipids produced from strains YM4, XY01, XY02, and XY03.

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Produced, Molecular Weight

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: Surface tension changes and CMC values of rhamnolipids produced by strain XY01 and YM4. The error bars represent standard deviation values of three independent experiments ( n = 3).

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Produced, Standard Deviation

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: The emulsifying activity of rhamnolipids produced by XY01 and YM4 on diesel oil at different concentrations.

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Activity Assay, Produced

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: Mono-rhamnolipid-producing strains and characteristics.

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Expressing

Journal: Molecules

Article Title: A Rare Mono-Rhamnolipid Congener Efficiently Produced by Recombinant Pseudomonas aeruginosa YM4 via the Expression of Global Transcriptional Regulator irrE

doi: 10.3390/molecules29091992

Figure Lengend Snippet: Strains and plasmids used in this study.

Article Snippet: Strain Pseudomonas aeruginosa YM4 (CCTCC M2017494) [ ] was an efficient rhamnolipids producer and used as the starting strain for molecular manipulation. provides a list of the strains and plasmids used in this work.

Techniques: Plasmid Preparation, Amplification, In Vivo

Journal: Nucleic Acids Research

Article Title: Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species

doi: 10.1093/nar/gkaf984

Figure Lengend Snippet: M13 PAB receptor-binding domain and binding to P. aeruginosa strains. ( A ) Amino acid sequence of the 92-amino acid RBD of M13 PAB phage. Residues 1–51 (purple), 52–70 (navy), and 71–92 (brown) are identical (100% sequence identity, 0 gaps) to the first and second fragments of RBD 24947 (24947–1, 24947–2) and the fifth fragment of RBD 50842 (50842–5), respectively, as mapped in panel (B). ( B ) Hypothesized origin of the M13 PAB RBD DNA sequence from Gibson assembly of three fragments. Insert_Apm_upstream and Insert_Apm_downstream are PCR priming sites used to amplify the assembled RBD; NotI and AgeI restriction sites were used to clone the insert into the phagemid. Lower-case x denotes nonoverlapping bases that contribute to the PAB coding sequence; upper-case X denotes overlapping sequences that contribute to the PAB coding sequence. The highlight color matches the DNA sequence with the amino acid sequence in panel (A). “=” indicates bases of 24947–2 that were absent from PAB. “+” indicates spacer bases in 50842–5 that were added for technical reasons (see the “Materials and methods” section). ( C ) Binding of M13 PAB phage with strains of P. aeruginosa . M13 PAB phage (10 11 virions) was incubated with 1 mL of cells at OD 600 = 1 (∼10 8 cells), and bound phage was quantified by qPCR after washing. Binding of each P. aeruginosa strain was compared to the yeast control. Significantly greater binding to P. aeruginosa was observed in all cases (Bonferroni-adjusted P -values for pairwise two-sided Welch t -tests: ATCC 25102, P < .001; C.S. A, P < .001; C.S. B, P = .035; C.S. C, P < .001; C.S. E, P = .002; C.S. F, P < .001; C.S. M, P = .007; pmrB6, P < .001). Data are mean ± SD ( n = 9 per group, three technical replicates for each of three experimental replicates). C.S. = clinical strain; pmr B6 = PAK pmr B6; yeast = S. cerevisiae ATCC204508/S288c (gray).

Article Snippet: To identify P. aeruginosa -binding clones, phages were produced from the Pa-RBD library (1 × 10 12 virions) and incubated with ∼4 × 10 8 CFU of bacteria from each of 15 different P. aeruginosa strains (ATCC 25102 and 14 clinical isolates; Table ).

Techniques: Binding Assay, Sequencing, Incubation, Control

Journal: Nucleic Acids Research

Article Title: Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species

doi: 10.1093/nar/gkaf984

Figure Lengend Snippet: M13 PAB phage bound to different P. aeruginosa strains visualized by TEM (negative stain). Since filamentous phages have similar morphology to bacterial structures such as pili, phages were specifically labeled with gold nanoparticles (dark spheres) coated with antibodies against pVIII, allowing phages (yellow darts) to be easily differentiated from other structures. Gold-labeled M13 PAB phages are shown ( A ) without bacteria; or incubated with P. aeruginosa strain: ( B ) ATCC 25102; ( C ) clinical strain A; ( D ) clinical strain B; ( E ) clinical strain C; and ( F ) polymyxin-resistant mutant PAK pmr B6. Note that phage width is increased by the labeling reagents. Scale bars = 500 nm.

Article Snippet: To identify P. aeruginosa -binding clones, phages were produced from the Pa-RBD library (1 × 10 12 virions) and incubated with ∼4 × 10 8 CFU of bacteria from each of 15 different P. aeruginosa strains (ATCC 25102 and 14 clinical isolates; Table ).

Techniques: Staining, Labeling, Bacteria, Incubation, Mutagenesis

Journal: Nucleic Acids Research

Article Title: Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species

doi: 10.1093/nar/gkaf984

Figure Lengend Snippet: PAB domain effects on binding to P. aeruginosa . ( A ) The highest-ranked predicted structure of PAB protein by AlphaFold2, with the N-terminus and C-terminus indicated. ( B ) Binding of M13 PAB and mutants M13 PAB -dNT (deleting N-terminal domain), M13 PAB -d α (deleting alpha helix), M13 PAB -d β (deleting beta sheet), and M13 PAB -dCT (deleting C-terminal domain) to P. aeruginosa ATCC 25102 when mixing 1 × 10 11 virions of phages with 1 mL of cells at OD 600 = 1 (OD 600 = 1 corresponds to ∼10 8 cells/mL) and incubating for 30 min at room temperature on a rotator. The amount of bound phage was measured by quantitative PCR. Bar height is the average of technical quadruplicate data on experimental duplicates, and error bars show 1 standard deviation. Significant loss of binding is caused by deletion of the N-terminal domain ( P < .0001, two-sided Welch t -test).

Article Snippet: To identify P. aeruginosa -binding clones, phages were produced from the Pa-RBD library (1 × 10 12 virions) and incubated with ∼4 × 10 8 CFU of bacteria from each of 15 different P. aeruginosa strains (ATCC 25102 and 14 clinical isolates; Table ).

Techniques: Binding Assay, Real-time Polymerase Chain Reaction, Standard Deviation

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: MIC data for Sphistin alone and in combination with antibiotics against P. aeruginosa .

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques:

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: MIC data for Sph 12−38 alone and in combination with antibiotics against P. aeruginosa .

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques:

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: Flow cytometry showing P. aeruginosa exposed to Sphistin, azithromycin, rifampicin, Sphistin in combination with azithromycin, and Sphistin in combination with rifampicin. The bacteria were all incubated with (A) 6 μmol L −1 Sphistin, (B) 18 μg·ml −1 azithromycin, (C) a combination of 6 μmol·L −1 Sphistin and 18 μg·ml −1 azithromycin for 4 h at 37°C; and (D) 1.5 μmol·L −1 Sphistin, (E) 0.625 μg·ml −1 rifampicin, (F) a combination of 1.5 μmol·L −1 Sphistin and 0.625 μg·ml −1 rifampicin for 2 h at 37°C. Then, the bacteria were all stained with SYTO 9 and propidium iodide (PI) fluorescent nucleic acid stain. (G) The same amounts of living bacteria and completely dead bacteria were stained with SYTO 9 and PI, respectively. Bacteria were stained with SYTO 9, which showed living cells in the Q1-LR quadrant, while those bacterial cells that were only stained with PI were all in the Q1-UL quadrant; in the Q1-UR quadrant, the bacterial cells were stained by the SYTO 9 and PI together. The results were detected by flow cytometry.

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques: Flow Cytometry, Bacteria, Incubation, Staining

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: Growth curves of P. aeruginosa when incubated with (A) DPBS, Sphistin (6 μmol·L −1 ), azithromycin (18 μg·ml −1 ), and Sphistin (6 μmol·L −1 ) in combination with azithromycin (18 μg·ml −1 ) for 2 h; (B) DPBS, Sphistin (1.5 μmol·L −1 ), rifampicin (0.625 μg·ml −1 ), and Sphistin (1.5 μmol·L −1 ) in combination with rifampicin (0.625 μg·ml −1 ) for 6 h.

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques: Incubation

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: Scanning electron microscope (SEM) images of P. aeruginosa treated with (A) 6 μmol·L −1 Sphistin, (B) 18 μg·ml −1 azithromycin, and (C) a combination of 6 μmol·L −1 Sphistin and 18 μg·ml −1 azithromycin for 2 h at 37°C. Meanwhile, the bacteria treated with (D) 1.5 μmol·L −1 Sphistin, (E) 0.625 μg·ml −1 rifampicin, (F) a combination of 1.5 μmol·L −1 Sphistin and 0.625 μg·ml −1 rifampicin, and (G) DPBS for 4 h at 37°C.

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques: Microscopy, Bacteria

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: Extracellular ATP release in different treatment groups after exposure of P. aeruginosa to (A) DPBS, Sphistin (6 μmol·L −1 ), and/or azithromycin (18 μg·ml −1 ) for 2 h; (B) DPBS, Sphistin (1.5 μmol·L −1 ), and/or rifampicin (0.625 μg·ml −1 ) for 4 h. The bacteria cell membrane damage induced by the antibacterial agents is accompanied by leakage of intracellular content due to compromised membrane integrity.

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques: Bacteria, Membrane

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: The Synergistic Effect of Mud Crab Antimicrobial Peptides Sphistin and Sph 12−38 With Antibiotics Azithromycin and Rifampicin Enhances Bactericidal Activity Against Pseudomonas Aeruginosa

doi: 10.3389/fcimb.2020.572849

Figure Lengend Snippet: Transmission electron microscopy (TEM) images of P. aeruginosa treated with (A) DPBS, (B) 6 μmol·L −1 Sphistin, (C) 18 μg·ml −1 azithromycin, and (D) a combination of 6 μmol·L −1 Sphistin and 18 μg·ml −1 azithromycin for 1 h at 37°C.

Article Snippet: The P. aeruginosa strain (ATCC 9027) was cultured at 37°C until the bacterial cells reached the logarithmic phase, and then the bacterial cells were harvested and washed twice using the NB.

Techniques: Transmission Assay, Electron Microscopy

Journal: PLoS ONE

Article Title: Internal Colonization of Salmonella enterica Serovar Typhimurium in Tomato Plants

doi: 10.1371/journal.pone.0027340

Figure Lengend Snippet: Statistical analysis of parameter estimates for the exponential decline of Salmonella enterica Typhimurium concentrations on/in tomato leaves over a 21 day period.

Article Snippet: Different from their wild type strain S. enterica Typhimurium ATCC 14208, MAE110 constantly presents the rdar morphotype, whereas MAE119 has completely lost the rdar morphotype and develops shiny and smooth colonies , , , .

Techniques:

Journal: PLoS ONE

Article Title: Internal Colonization of Salmonella enterica Serovar Typhimurium in Tomato Plants

doi: 10.1371/journal.pone.0027340

Figure Lengend Snippet: Salmonella enterica Typhimurium contamination in tomato plants.

Article Snippet: Different from their wild type strain S. enterica Typhimurium ATCC 14208, MAE110 constantly presents the rdar morphotype, whereas MAE119 has completely lost the rdar morphotype and develops shiny and smooth colonies , , , .

Techniques:

Journal: PLoS ONE

Article Title: Internal Colonization of Salmonella enterica Serovar Typhimurium in Tomato Plants

doi: 10.1371/journal.pone.0027340

Figure Lengend Snippet: Statistical analysis of parameter values for a Gompertz growth curve of Salmonella enterica Typhimurium in tomato fruits after peduncle injection.

Article Snippet: Different from their wild type strain S. enterica Typhimurium ATCC 14208, MAE110 constantly presents the rdar morphotype, whereas MAE119 has completely lost the rdar morphotype and develops shiny and smooth colonies , , , .

Techniques: Injection

Journal: PLoS ONE

Article Title: Internal Colonization of Salmonella enterica Serovar Typhimurium in Tomato Plants

doi: 10.1371/journal.pone.0027340

Figure Lengend Snippet: Salmonella enterica Typhimurium. SDW: Sterile distilled water.

Article Snippet: Different from their wild type strain S. enterica Typhimurium ATCC 14208, MAE110 constantly presents the rdar morphotype, whereas MAE119 has completely lost the rdar morphotype and develops shiny and smooth colonies , , , .

Techniques: Sterility