Journal: Scientific Reports

Article Title: Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids

doi: 10.1038/s41598-022-18460-w

Figure Lengend Snippet: Applications of cationic styryl dyes for DNA detection in vitro ( a – e ) and for cellular nucleic acid detection ( f ). Sensitivity ( a , b ) and specificity ( c , d ) test of E. coli ( a , c ) and S. aureus ( b , d ) detection based on LAMP- 4QL2+ assay, and gel electrophoresis results from the E. coli sensitivity assay ( e ). Lanes in ( a ), ( e ) 1 : negative control, 2 : 3.39 × 10 −1 , 3 : 3.39 × 10 0 , 4 : 3.39 × 10 1 , 5 : 3.39 × 10 2 , 6 : 3.39 × 10 3 copies of DNA/reaction; ( b ) 1 : negative control, 2 : 3.3 × 10 −2 , 3 : 3.3 × 10 −1 , 4 : 3.3 × 10 0 , 5 : 3.3 × 10 1 , 6 : 3.3 × 10 2 copies of DNA/reaction; ( c ) 1 : E. coli ATCC 25922, 2 : E. coli MCCU0349, 3 : E. cloacae , 4 : S. aureus ATCC 25923, 5 : S. epidermidis ATCC 12228, d) 1 : S. aureus ATCC 25923, 2 : S. aureus MCCU0357, 3 : S. aureus MCCU0370 sample; 4 : S. epidermidis ATCC 12228, 5 : S. saprophyticus ATCC 15305, 6 : E. coli ATCC 25922. ( f ) Fluorescence images of HeLa cells stained with BT2+(NEt 2 ) and SYTO RNA select® Green (as individual dyes or co-stained). The cells were co-stained with DAPI in all cases (blue channel). Scale bars = 10 µm.

Article Snippet: For the sensitivity assays, 10-fold serial dilutions of E. coli ATCC 25922 (3.39 × 10 3 –0.339 copies of DNA), and S. aureus ATCC 25923 (3.3 × 10 2 –0.033 copies of DNA) were used as a template to determine the minimum amounts of template DNA that can be detected by LAMP- 4QL2+ assay.

Techniques: In Vitro, Nucleic Acid Electrophoresis, Sensitive Assay, Negative Control, Fluorescence, Staining

Journal: ACS Infectious Diseases

Article Title: Insights into the Spectrum of Activity and Mechanism of Action of MGB-BP-3

doi: 10.1021/acsinfecdis.2c00445

Figure Lengend Snippet: Thermal melt curves of gDNA (salmon) and gDNA:MGB-BP-3 Complex. (A) Exemplar melt curve from one experimental repeat, visually representing the different melt curves of gDNA and the gDNA:MGB-BP-3 Complex. Data has been fitted with a Boltzmann distribution. (B) Melting temperatures of gDNA and gDNA:MGB-BP-3 Complex calculated from fitted Boltzmann distributions using OriginPro 2021. All values are an average for n = 4 experimental repeats with an error of ±1 °C.

Article Snippet: Bacterial genomic DNA (ATCC 43300, DSM 13661; ATCC 27853, DSM1117; ATCC 700603, DSM 26371; ATCC 25922, DSM 1103; ATCC 19606, DSM 30007; ATCC 51299, DSM 12956; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH) or salmon genomic DNA (deoxyribonucleic acid sodium salt from salmon testes, D1626, Merck) dissolved in 1 mM phosphate buffer pH 7.4 (containing 0.27 mM potassium chloride, 13.7 mM sodium chloride) to a concentration of 100 μg/mL in SybrSafe (SYBR Safe DNA Gel Stain, ×10,000 in DMSO, S33102 Invitrogen) was used as supplied by the manufacturer in DMSO, and MGB-BP-3 was prepared as 10 mM stock in DMSO.

Techniques:

Journal: ACS Infectious Diseases

Article Title: Insights into the Spectrum of Activity and Mechanism of Action of MGB-BP-3

doi: 10.1021/acsinfecdis.2c00445

Figure Lengend Snippet: Remaining Fluorescence (%) of SybrSafe Probe upon Addition of MGB-BP-3 to gDNA a

Article Snippet: Bacterial genomic DNA (ATCC 43300, DSM 13661; ATCC 27853, DSM1117; ATCC 700603, DSM 26371; ATCC 25922, DSM 1103; ATCC 19606, DSM 30007; ATCC 51299, DSM 12956; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH) or salmon genomic DNA (deoxyribonucleic acid sodium salt from salmon testes, D1626, Merck) dissolved in 1 mM phosphate buffer pH 7.4 (containing 0.27 mM potassium chloride, 13.7 mM sodium chloride) to a concentration of 100 μg/mL in SybrSafe (SYBR Safe DNA Gel Stain, ×10,000 in DMSO, S33102 Invitrogen) was used as supplied by the manufacturer in DMSO, and MGB-BP-3 was prepared as 10 mM stock in DMSO.

Techniques: Fluorescence

Journal: Nanomaterials

Article Title: Effect of Size and Concentration of Copper Nanoparticles on the Antimicrobial Activity in Escherichia coli through Multiple Mechanisms

doi: 10.3390/nano12213715

Figure Lengend Snippet: Bactericidal activities of CuNPs. E. coli were treated with different concentrations of CuNPs of 20 nm or 60 nm size. Bacteria treated with PBS or 70% alcohol were used as the negative and positive controls, respectively. ( a , b ) Determination of E. coli growth by optical density measurement. Cell growth curves from 0 to 12 h were analyzed with absorbance at 600 nm wavelength. Statistical calculation after treatment for 12 h was analyzed. ( c ) The percentage of colony formation of E. coli recovered after treatment with CuNPs for 24 h. ( d ) Bacterial viability analysis with PrestoBlue assay after treatment with CuNPs for 24 h. Bioactivities were determined at the emitting fluorescence of 590 nm. In both ( c , d ), one hundred percent value corresponds to the number in the negative control. Data are presented as mean ± SD from three independent experiments performed in triplicate for each treatment group. Statistical comparisons were performed by Student’s t -test; α and β indicate p < 0.05 for 20 and 60 nm CuNP treatments relative to the negative control, respectively, and * indicates p < 0.05 for comparisons between 20 and 60 nm of CuNPs in ( c , d ).

Article Snippet: E. coli (Migula) Castellani and Chalmers strain 25922 was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in Luria–Bertani (LB) broth (Becton, Dickinson and Company, Sparks, MD, USA) or LB agar (FocusBio, Miaoli, Taiwan).

Techniques: Bacteria, Prestoblue Assay, Fluorescence, Negative Control

Journal: Nanomaterials

Article Title: Effect of Size and Concentration of Copper Nanoparticles on the Antimicrobial Activity in Escherichia coli through Multiple Mechanisms

doi: 10.3390/nano12213715

Figure Lengend Snippet: Electron microscopy images of E. coli treated with two sizes of CuNPs in different concentrations. Cells treated with PBS or 70% alcohol served as the negative control and positive control, respectively. ( a , b ) Live or dead cells observed via SEM. Images were obtained using a S-4700 SEM with a magnification of 30,000×. Arrow heads indicate the wrinkles of cell membranes; arrows mark the cracks on plasma membranes; stars illustrate the cytoplasmic components leaking from cells. Scale bar = 1 μm ( c , d ) Live or dead cells observed via TEM. Images were obtained using an H-7500 TEM with a magnification of 30,000×. Two percent of uranyl acetate was applied for the negative stain of cells followed by TEM imaging. Arrows indicate the membrane damage. Scale bar = 500 nm.

Article Snippet: E. coli (Migula) Castellani and Chalmers strain 25922 was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in Luria–Bertani (LB) broth (Becton, Dickinson and Company, Sparks, MD, USA) or LB agar (FocusBio, Miaoli, Taiwan).

Techniques: Electron Microscopy, Negative Control, Positive Control, Clinical Proteomics, Staining, Imaging, Membrane

Journal: Nanomaterials

Article Title: Effect of Size and Concentration of Copper Nanoparticles on the Antimicrobial Activity in Escherichia coli through Multiple Mechanisms

doi: 10.3390/nano12213715

Figure Lengend Snippet: Membrane leakage detection in bacteria after being treated with two sizes of CuNPs in different concentrations for 24 h. ( a ) Flow cytometry profile of the bacterial population in control groups stained with PI dye. E. coli treated with PBS served as the negative control. E. coli treated with 70% alcohol plus triton X-100 or autoclaving served as positive controls. ( b ) Membrane permeability of E. coli . After CuNP treatment, PI staining was applied then analyzed using flow cytometry. ( c ) Cytoplasmic protein leakages in E. coli after CuNP treatment. Leaking proteins were collected from supernatants and detected by Bradford protein assay at an absorbance of 595 nm. Data are presented as mean ± SD from three independent experiments performed in triplicate for each treatment group. Statistical comparisons were performed by Student’s t -test; α and β indicate p < 0.05 for 20 and 60 nm CuNP treatments relative to negative control, respectively.

Article Snippet: E. coli (Migula) Castellani and Chalmers strain 25922 was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in Luria–Bertani (LB) broth (Becton, Dickinson and Company, Sparks, MD, USA) or LB agar (FocusBio, Miaoli, Taiwan).

Techniques: Membrane, Bacteria, Flow Cytometry, Control, Staining, Negative Control, Permeability, Bradford Protein Assay

Journal: Nanomaterials

Article Title: Effect of Size and Concentration of Copper Nanoparticles on the Antimicrobial Activity in Escherichia coli through Multiple Mechanisms

doi: 10.3390/nano12213715

Figure Lengend Snippet: ROS generation in E. coli after CuNP treatment. ( a ) Flow cytometry analysis of ROS induced by various inducers in E. coli . Four groups of bacteria were subjected to the following conditions to induce ROS: 405 nm UV light for 3 h, 45 °C for 2 h, 4 °C for 2 h, and 3% H 2 O 2 for 30 min. Bacteria cultured under normal conditions (37 °C, LB medium) and then washed with PBS served as the negative control. H 2 DCFDA was applied to bacteria to detect ROS. ( b ) Fractions of fluorescent positive cells in different CuNP treatments. Bacteria were treated with two sizes of CuNPs in different concentrations for 24 h and then stained with H 2 DCFDA. Fluorescence was detected by flow cytometry. These data are presented as mean ± SD from five independent experiments performed in triplicate for each treatment group. Statistical comparisons were performed by Student’s t -test; α and β indicate p < 0.05 for 20 and 60 nm CuNP treatments relative to the negative control, respectively, and * indicates p < 0.05 for the comparisons between 20 and 60 nm of CuNPs.

Article Snippet: E. coli (Migula) Castellani and Chalmers strain 25922 was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in Luria–Bertani (LB) broth (Becton, Dickinson and Company, Sparks, MD, USA) or LB agar (FocusBio, Miaoli, Taiwan).

Techniques: Flow Cytometry, Bacteria, Cell Culture, Negative Control, Staining, Fluorescence

Journal: Nanomaterials

Article Title: Effect of Size and Concentration of Copper Nanoparticles on the Antimicrobial Activity in Escherichia coli through Multiple Mechanisms

doi: 10.3390/nano12213715

Figure Lengend Snippet: Total genomic DNA analysis of E. coli via electrophoresis. Chromosomal DNA damages were detected in bacteria treated with 20 nm CuNPs ( a ), or 60 nm CuNPs ( b ), in a series of concentrations (0, 1, 5, 10, 50, 100 μg/mL) for 24 h followed by genomic DNA extraction. Ten μg/mL AgNPs and 5 μg/mL Amp were incubated with bacteria for 3 h to induce condensation of DNA and early apoptosis in E. coli . Autoclaving and 70% alcohol treatments were applied to induce acute cell death. PBS treatment was used as a negative control (NC) in the study of cell survival and chromosomal DNA integrity. One kb DNA ladder was loaded as the marker (M). The arrows indicated the positions of chromosomal DNA, 23S rRNA, and 16S rRNA. Orange frames marked the condensed DNA. DNAs were analyzed by agarose-based gel electrophoresis, and a Gel Doc EZ imaging system was used to obtain images.

Article Snippet: E. coli (Migula) Castellani and Chalmers strain 25922 was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in Luria–Bertani (LB) broth (Becton, Dickinson and Company, Sparks, MD, USA) or LB agar (FocusBio, Miaoli, Taiwan).

Techniques: Electrophoresis, Bacteria, DNA Extraction, Incubation, Negative Control, Marker, Agarose Gel Electrophoresis, Imaging

Journal: Nanomaterials

Article Title: Effect of Size and Concentration of Copper Nanoparticles on the Antimicrobial Activity in Escherichia coli through Multiple Mechanisms

doi: 10.3390/nano12213715

Figure Lengend Snippet: Flow cytometry analysis of annexin V-PI staining in E. coli after CuNP treatment. ( a ) E. coli was treated with PBS (negative control), autoclaving, 10 μg/mL AgNPs, and 5 μg/mL Amp, followed by annexin V-PI staining. FL1 and FL3 were regarded as annexin V and PI signals. ( b ) Different fractions of positive cells from quadrants. Bacteria were treated with two sizes of CuNPs in different concentrations for 24 h. Bacteria treated with PBS served as the negative control. Fluorescent intensity was acquired by flow cytometry, and single positive (FL1 + /FL3 − ; FL1 − /FL3 + ) as well as double positive (FL1 + /FL3 + ) signals were calculated. ( c ) Statistical analysis of apoptosis bacterial cells which were represented by the sum of percentages from FL1 + /FL3 − (early stage) and FL1 + /FL3 + (late stage). Data were presented as mean ± SD from six independent experiments performed in triplicate for each treatment group. Data were analyzed by the Kruskal–Wallis H test followed by Dunn’s post hoc test; α and β indicate p < 0.05 for 20 and 60 nm CuNP treatments relative to the negative control, respectively. Statistical difference between 20 and 60 nm CuNP treatments was set at p < 0.05 (*) according to the paired t -test.

Article Snippet: E. coli (Migula) Castellani and Chalmers strain 25922 was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in Luria–Bertani (LB) broth (Becton, Dickinson and Company, Sparks, MD, USA) or LB agar (FocusBio, Miaoli, Taiwan).

Techniques: Flow Cytometry, Staining, Negative Control, Bacteria