e coli dh5α strain  (ATCC)

Journal: Applied and Environmental Microbiology

Article Title: A recombineering-based platform for high-throughput genomic editing in Escherichia coli

doi: 10.1128/aem.00193-25

Figure Lengend Snippet: Large-fragment deletion in E. coli MG1655 and E. coli Nissle 1917. ( A ) Genomic editing tests of sequence deletion of different lengths in MG1655. ( B ) E. coli MG1655 genomic editing results of sequence deletion of different sizes. ( C ) Deletion of E. coli MG1655 large fragments in different genomic locations. ( D ) Genomic editing tests of sequence deletion of different lengths in EcN. ( E ) EcN genomic editing results of sequence deletion of different sizes. (F through H) The sequencing results of 10 kb, 22 kb, and 58 kb fragment deletions.

Article Snippet: E. coli strain DH5α (ATCC 68233) served as the host strain for molecular cloning and plasmid manipulation.

Techniques: Sequencing

Journal: Biosensors & bioelectronics

Article Title: Rapid and sensitive biosensing of uropathogenic E. coli using plasmonic nanohole arrays on MIM: Bridging the gap between lab and clinical diagnostics.

doi: 10.1016/j.bios.2025.117419

Figure Lengend Snippet: Fig. 4. A Surface biofunctionalization of plasmonic MIM NHA biosensors. (left) Normalized reflectance spectra after each immobilization step B Antibody and immobilization route selection. Error bars respesents ±σ. The three replicates (n = 3) were analyzed in separate SPR channels. C SEM micrograph of uropathogenic E. coli on plasmonic MIM NHA biosensors. D Biosensing performance of plasmonic MIM NHA biosensors. The blank response statistics of the biosensor (left). The box chart range repesents ±σ. The whiskers represent 5 and 95 percentile. The normal distribution is presented on the right of the box chart. The plasmon resonance wavelength dip change is presented for the selection of pathogens (Uropathogenic E. coli, E. coli K12, S. aureus, C. freundii, and P. mirabilis) within the logarithmic concentration range of 1–106 cfu mL−1 (middle) Normalized biosensor response for selected pathogens and fitted Hill-Langmuir curve for uropathogenic E. coli case. (right) The error bar of each individual point represents ±σ for n = 5.

Article Snippet: To assess the specificity and selectivity of the system, we also evaluated the binding characteristics of E. coli K12 (ATCC-PTA-7555), S. aureus (ATCC-15305), C. freundii (ATCC-8090), and P. mirabilis (ATCC-51286) at logarithmic concentration range of 1–106 cfu mL− 1 (Fig. 4D).

Techniques: Selection, Concentration Assay

Journal: Biosensors & bioelectronics

Article Title: Rapid and sensitive biosensing of uropathogenic E. coli using plasmonic nanohole arrays on MIM: Bridging the gap between lab and clinical diagnostics.

doi: 10.1016/j.bios.2025.117419

Figure Lengend Snippet: Fig. 5. A The binary classification of clinically tested uropathogenic E. coli (UPEC) negative and positive samples with respect to the plasmon resonance wavelength shift (Δλ). The clinical data set has a cohort of 100 individuals consisting of clinically diagnosed 50 UPEC+ and 50 UPEC−. The UPEC + cohort had 13 male and 37 female patients. The UPEC + cohort had 9 male and 41 female patients. The statistical significance (p < 0.005) was calculated using both Welch’s t-test and Mann- Whitney U Test. B The multiclass classification of UPEC−, UPEC + results with a UPEC concentration of <104, ~105, and >105 cfu mL−1 with respect to the normalized response of the PANTOMIM biosensor. The box chart height represents ±σ error bars, and the left-hand side curve represents the normal distribution. The values on the right and left side of the box chart represent the mean of the distribution with respect to resonance wavelength shift and normalized response, respectively. The horizontal line in the box chart represents the median of the statistical population. The box chart range repesents ±σ. The whiskers represent 5 and 95 percentile. The normal distribution is presented on the right of the box chart. The mean value is represent on the right side as well. C The receiver operational characteristics (ROC) of PANTOMIM biosensor in binary classification of clinical samples. The accuracy and F1 predictive performance depend on the normalized response cut-offs. (right) The absolute and specific limit of detection (LoD) levels extracted from the in-vitro calibration curve are annotated in both figures. The shaded areas show 99 % and 95 % confidence intervals for ROC analysis and accuracy/F1 performance, respectively. D The normalized response of PANTOMIM biosensor for 50 clinically UPEC− samples. (top) The total cell and leukocyte counts from the clinical samples are presented in the log scale (bottom). E The normalized response of PANTOMIM biosensor for 50 clinically UPEC + samples. (top) The total cell and leukocyte counts from the clinical samples are presented in the log scale (bottom). The clinically detected UPEC levels for unannotated samples are 105 cfu mL−1. The different levels are annotated using red, orange, and yellow circles for >105, ~5 × 104, and <104 cfu mL−1, respectively. For all UPEC + samples, gram− bacilli and leukocytes were present in microscopic analysis. The presence of both species and interferants are annotated above section E.

Article Snippet: To assess the specificity and selectivity of the system, we also evaluated the binding characteristics of E. coli K12 (ATCC-PTA-7555), S. aureus (ATCC-15305), C. freundii (ATCC-8090), and P. mirabilis (ATCC-51286) at logarithmic concentration range of 1–106 cfu mL− 1 (Fig. 4D).

Techniques: MANN-WHITNEY, Concentration Assay, In Vitro