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Zymo Research methylated genomic dna
Methylated Genomic Dna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 93/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/methylated genomic dna/product/Zymo Research
Average 93 stars, based on 29 article reviews

methylated genomic dna - by Bioz Stars, 2026-03

93/100 stars

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Growth curves and intracellular thiol analysis E. coli ATCC 25922 growth curves and intracellular thiol analysis in the presence of compounds 3d (red), 3l (dark yellow), and 3n (green) at the static MICs (A and B) and at 3-fold static MICs (C and D). Cultures grown in the presence of 1% DMSO (white) and 5 mM (345 μg/mL) 1,2,4-triazole (gray) were included as negative and positive controls, respectively. The bars represent the average of at least 3 biological replicates, and the error bars represent the SD. The statistical significance of thiol decrease was determined by a two-way ANOVA test (see ). ∗ p < 0.1; ∗∗ p < 0.01; ∗∗∗ p < 0.001.

Journal: iScience

Article Title: Benzotriazole derivatives as alternate O- acetylserine sulfhydrylase substrates to impair cysteine biosynthesis in gram-negative bacteria

doi: 10.1016/j.isci.2025.113818

Figure Lengend Snippet: Growth curves and intracellular thiol analysis E. coli ATCC 25922 growth curves and intracellular thiol analysis in the presence of compounds 3d (red), 3l (dark yellow), and 3n (green) at the static MICs (A and B) and at 3-fold static MICs (C and D). Cultures grown in the presence of 1% DMSO (white) and 5 mM (345 μg/mL) 1,2,4-triazole (gray) were included as negative and positive controls, respectively. The bars represent the average of at least 3 biological replicates, and the error bars represent the SD. The statistical significance of thiol decrease was determined by a two-way ANOVA test (see ). ∗ p < 0.1; ∗∗ p < 0.01; ∗∗∗ p < 0.001.

Article Snippet: E. coli MG1655 , ATCC , N/A.

Techniques:

Fractional inhibitory concentration (FIC) index of the best combinations among 3d , 3l , and 3n BT derivatives with different antibiotics Antibiotic-BT derivatives were tested on E. coli ATCC 25922 (magenta), S. Typhimurium ATCC 14028 (violet), and K. pneumoniae ATCC 13883 (light blue). The data represent the FIC index between colistin, gentamicin, ciprofloxacin, or ampicillin and the most effective concentration of BT derivative. An FIC index ≤0.5 is indicative of synergy of action, 0.5 < FIC ≤1 shows additivity of action, and 1 < FIC <4 shows indifference between the couples of considered compounds. The complete set of data is reported in .

Journal: iScience

Article Title: Benzotriazole derivatives as alternate O- acetylserine sulfhydrylase substrates to impair cysteine biosynthesis in gram-negative bacteria

doi: 10.1016/j.isci.2025.113818

Figure Lengend Snippet: Fractional inhibitory concentration (FIC) index of the best combinations among 3d , 3l , and 3n BT derivatives with different antibiotics Antibiotic-BT derivatives were tested on E. coli ATCC 25922 (magenta), S. Typhimurium ATCC 14028 (violet), and K. pneumoniae ATCC 13883 (light blue). The data represent the FIC index between colistin, gentamicin, ciprofloxacin, or ampicillin and the most effective concentration of BT derivative. An FIC index ≤0.5 is indicative of synergy of action, 0.5 < FIC ≤1 shows additivity of action, and 1 < FIC <4 shows indifference between the couples of considered compounds. The complete set of data is reported in .

Article Snippet: E. coli MG1655 , ATCC , N/A.

Techniques: Concentration Assay

Vaginal infections and psychoactive substance use as contributing factors for E. coli urinary tract infection. G. vaginalis and C. albicans are known to cause vaginal infections in women during reproductive age; these microorganisms cause an increase in urinary pH, decrease in the genitourinary proportion of Lactobacillus spp and enhance uroepithelial exfoliation and apoptosis, promoting the growth and development of E. coli urinary tract infections. Additionally, the use of psychoactive substance impacts the immune system response by decreasing humoral and cell-mediated immunity and increasing the synthesis of pro-inflammatory cytokines leading to UTI by E. coli. *Please note that the figure presented was created using BioRender and serves as a summary of the observed results in this research

Journal: BMC Pregnancy and Childbirth

Article Title: Association of substance use and vaginal infection with UTI in adolescent pregnant patients: a retrospective study

doi: 10.1186/s12884-025-08364-8

Figure Lengend Snippet: Vaginal infections and psychoactive substance use as contributing factors for E. coli urinary tract infection. G. vaginalis and C. albicans are known to cause vaginal infections in women during reproductive age; these microorganisms cause an increase in urinary pH, decrease in the genitourinary proportion of Lactobacillus spp and enhance uroepithelial exfoliation and apoptosis, promoting the growth and development of E. coli urinary tract infections. Additionally, the use of psychoactive substance impacts the immune system response by decreasing humoral and cell-mediated immunity and increasing the synthesis of pro-inflammatory cytokines leading to UTI by E. coli. *Please note that the figure presented was created using BioRender and serves as a summary of the observed results in this research

Article Snippet: E. coli genomic DNA was isolated using Quick-gDNATM MiniPrep (Zymo Research, USA) according to the manufacturer’s instructions, and isolates were classified into four phylogenetic groups using 100 ng of DNA in the multiplex-PCR described by Clermont et al. [ ].

Techniques: Infection

The multi-functional DHAP shunt of E. coli . ( A ) Genomic organization of the DHAP shunt operon and neighboring genes in E. coli ATCC 25922. The operon specifically consists of mtnK , mtnA , ald2 , and an annotated permease of unknown function . The pfs gene, conserved across all E. coli , is encoded in a different region of the E. coli genome. ( B ) Multiple sequence alignment of the DHAP shunt 5′-UTR region from 1,569 E. coli genomes containing the DHAP shunt operon. Positions matching the ATCC 25922 reference are shown in gray, while mismatches are shown in red. ( C and D ) Biochemical reactions catalyzed by the DHAP shunt pathway enzymes, with 5′-deoxyadenosine ( C ) or 5′-methylthioadenosine ( D ) as initial substrate.

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: The multi-functional DHAP shunt of E. coli . ( A ) Genomic organization of the DHAP shunt operon and neighboring genes in E. coli ATCC 25922. The operon specifically consists of mtnK , mtnA , ald2 , and an annotated permease of unknown function . The pfs gene, conserved across all E. coli , is encoded in a different region of the E. coli genome. ( B ) Multiple sequence alignment of the DHAP shunt 5′-UTR region from 1,569 E. coli genomes containing the DHAP shunt operon. Positions matching the ATCC 25922 reference are shown in gray, while mismatches are shown in red. ( C and D ) Biochemical reactions catalyzed by the DHAP shunt pathway enzymes, with 5′-deoxyadenosine ( C ) or 5′-methylthioadenosine ( D ) as initial substrate.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Functional Assay, Sequencing

Regulation of E. coli ATCC 25922 transcriptome during growth on glucose, 5dR, or carbon starvation. Volcano plots of changes in ATCC 25922 transcript abundance for ( A ) wild-type ATCC 25922 grown with 5dR versus glucose, ( B ) MtnR deletion strain (∆ mtnR ) versus wild-type ATCC 25922 grown with glucose, and ( C ) ATCC 25922 incubated under carbon starvation conditions versus carbon replete (glucose) conditions. Gray lines indicate 2.5 log 2 -fold change thresholds; DHAP shunt genes are highlighted in pink. ( A ) DHAP shunt genes are strongly upregulated (~7.5 log 2 ) in the presence of 5dR. ( B ) Deletion of MtnR (∆ mtnR ) results in ~5 log 2 increased expression of DHAP shunt genes compared to the wild-type strain in the presence of glucose. ( C ) Carbon starvation only moderately upregulated DHAP shunt gene expression. ( D ) Inventory of genes differentially expressed under 5dR growth and carbon starvation relative to growth on glucose. Carbon starvation triggers a large change in the proteome compared to growth on 5dR, indicating the proteome change during growth on 5dR is specific to the substrate and not a general stress response.

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: Regulation of E. coli ATCC 25922 transcriptome during growth on glucose, 5dR, or carbon starvation. Volcano plots of changes in ATCC 25922 transcript abundance for ( A ) wild-type ATCC 25922 grown with 5dR versus glucose, ( B ) MtnR deletion strain (∆ mtnR ) versus wild-type ATCC 25922 grown with glucose, and ( C ) ATCC 25922 incubated under carbon starvation conditions versus carbon replete (glucose) conditions. Gray lines indicate 2.5 log 2 -fold change thresholds; DHAP shunt genes are highlighted in pink. ( A ) DHAP shunt genes are strongly upregulated (~7.5 log 2 ) in the presence of 5dR. ( B ) Deletion of MtnR (∆ mtnR ) results in ~5 log 2 increased expression of DHAP shunt genes compared to the wild-type strain in the presence of glucose. ( C ) Carbon starvation only moderately upregulated DHAP shunt gene expression. ( D ) Inventory of genes differentially expressed under 5dR growth and carbon starvation relative to growth on glucose. Carbon starvation triggers a large change in the proteome compared to growth on 5dR, indicating the proteome change during growth on 5dR is specific to the substrate and not a general stress response.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Incubation, Expressing, Gene Expression

DHAP shunt 5′-UTR regions required for operon expression and repression by MtnR. ( A ) E. coli ATCC 25922 DHAP shunt genomic context and sections of 5′-UTR used for construction of plasmids (pLacZ###) with promoter– lacZ fusions. ( B, D ) LacZ activity assays from cell extracts of wild-type E. coli ATCC 25922 and ( C, E ) LacZ activity assays from cell extracts of MtnR deletion strain (Δ mtnR ) containing the indicated DHAP shunt 5′-UTR– lacZ fusion plasmids when grown with either 5 mM glucose (Glc), 5 mM glucose plus 5 mM 5dR (Glc + 5dR), or 5dR as the carbon source. The pLacZ control is a Lac promoter– lacZ fusion without added IPTG. Average and standard deviation error bars are for n = 3 independent replicates. ** P > 0.05, * P > 0.1; two-tailed t -test. ( F ) Log 2 -fold change in mtnK mRNA expression from transcriptomic analysis ( ; ) and measured by qRT-PCR for wild-type ATCC 25922 (WT), mtnR deletion strain (Δ mtnR ), and mtnR deletion strain complemented with mtnR from a plasmid (Δ mtnR + pmtnR). Tetracycline (10 ng/mL) was added to induce expression of mtnR from pmtnR plasmid. qRT-PCR average and standard deviation error bars are for n = 4 independent biological replicates except for WT Glc + 5dR versus Glc ( n = 8) and Δ mtnR + pmtnR Glc + 5dR versus Glc ( n = 3). ** P > 0.05; two-tailed t -test.

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: DHAP shunt 5′-UTR regions required for operon expression and repression by MtnR. ( A ) E. coli ATCC 25922 DHAP shunt genomic context and sections of 5′-UTR used for construction of plasmids (pLacZ###) with promoter– lacZ fusions. ( B, D ) LacZ activity assays from cell extracts of wild-type E. coli ATCC 25922 and ( C, E ) LacZ activity assays from cell extracts of MtnR deletion strain (Δ mtnR ) containing the indicated DHAP shunt 5′-UTR– lacZ fusion plasmids when grown with either 5 mM glucose (Glc), 5 mM glucose plus 5 mM 5dR (Glc + 5dR), or 5dR as the carbon source. The pLacZ control is a Lac promoter– lacZ fusion without added IPTG. Average and standard deviation error bars are for n = 3 independent replicates. ** P > 0.05, * P > 0.1; two-tailed t -test. ( F ) Log 2 -fold change in mtnK mRNA expression from transcriptomic analysis ( ; ) and measured by qRT-PCR for wild-type ATCC 25922 (WT), mtnR deletion strain (Δ mtnR ), and mtnR deletion strain complemented with mtnR from a plasmid (Δ mtnR + pmtnR). Tetracycline (10 ng/mL) was added to induce expression of mtnR from pmtnR plasmid. qRT-PCR average and standard deviation error bars are for n = 4 independent biological replicates except for WT Glc + 5dR versus Glc ( n = 8) and Δ mtnR + pmtnR Glc + 5dR versus Glc ( n = 3). ** P > 0.05; two-tailed t -test.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Expressing, Activity Assay, Control, Standard Deviation, Two Tailed Test, Quantitative RT-PCR, Plasmid Preparation

DHAP shunt expression is not activated by other alternative growth substrates. LacZ activity assays from cell extracts of E. coli ATCC 25922 containing the DHAP shunt 5′-UTR– lacZ fusion plasmid placZ255 and grown with either 5 mM glucose, NANA, l -fucose, l -arabinose, l -rhamnose, or 5-deoxy- d -ribose (5dR) as the sole carbon source. Average and standard deviation error bars are for n = 3 independent replicates. ** P > 0.05.

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: DHAP shunt expression is not activated by other alternative growth substrates. LacZ activity assays from cell extracts of E. coli ATCC 25922 containing the DHAP shunt 5′-UTR– lacZ fusion plasmid placZ255 and grown with either 5 mM glucose, NANA, l -fucose, l -arabinose, l -rhamnose, or 5-deoxy- d -ribose (5dR) as the sole carbon source. Average and standard deviation error bars are for n = 3 independent replicates. ** P > 0.05.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Expressing, Activity Assay, Plasmid Preparation, Standard Deviation

CRP is required for growth of E. coli ATCC 25922 using 5dR as a substrate. ( A and B ) Growth of wild-type ATCC 25922 (diamonds), CRP deletion strain (Δ crp ; triangles), and CRP deletion strain complemented with crp expressed from a plasmid (Δ crp + pCRP; circles) with ( A ) 5dR or ( B ) glucose as the sole carbon source. Average and standard deviation error bars are for n = 4 for growth on 5dR and n = 5 for growth on glucose. ( C ) Diauxic growth observed when wild-type ATCC 25922 is grown on a combination of 1 mM glucose plus 8 mM 5dR (diamonds), as compared to cultures grown with 1 mM glucose (triangles) or 8 mM 5dR (circles) as the sole carbon source. Dotted lines and fit parameters are for exponential regression fit to the growth data. Average and standard deviation error bars are for n = 5 independent biological replicates.

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: CRP is required for growth of E. coli ATCC 25922 using 5dR as a substrate. ( A and B ) Growth of wild-type ATCC 25922 (diamonds), CRP deletion strain (Δ crp ; triangles), and CRP deletion strain complemented with crp expressed from a plasmid (Δ crp + pCRP; circles) with ( A ) 5dR or ( B ) glucose as the sole carbon source. Average and standard deviation error bars are for n = 4 for growth on 5dR and n = 5 for growth on glucose. ( C ) Diauxic growth observed when wild-type ATCC 25922 is grown on a combination of 1 mM glucose plus 8 mM 5dR (diamonds), as compared to cultures grown with 1 mM glucose (triangles) or 8 mM 5dR (circles) as the sole carbon source. Dotted lines and fit parameters are for exponential regression fit to the growth data. Average and standard deviation error bars are for n = 5 independent biological replicates.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Plasmid Preparation, Standard Deviation

a . Diagram of key molecules in the chemotaxis network. Extracellular ligands (black semicircles) bind to receptors and modulate the activity of CheA, the kinase that phosphorylates the diffusible messenger CheY. CheA activity adaptation is mediated by the methylase CheR and de-methylase CheB. CheY-P binds to the C-ring and triggers a conformational change that results in BFM changing direction (CCW → CW). The swimming bacterium switches from a smooth run to a tumble. b . AlphaFold structure predictions of chimeric molecules. Grey is E. coli CheY, blue is cpAsLOV2, black is a short linker, and orange is the FliM peptide. Cartoons depicting the “caged” dark-state of Opto-CheY and the constitutively active control are shown with the same color code. c . Blue-light absorption triggers unfolding of the J α helix, and CheY activation by removal of the FliM plug from the CheY active site. Active CheY binds to the C-ring and promotes the rotational switch of the BFM from CCW → CW. Light pulses (blue dots, ~100 µ J/cm 2 ) are applied every 6 seconds while monitoring BFM rotational state. Each response is a CW rotation (vertical black line) following a blue light pulse (blue dot) in an otherwise mostly CCW motor (bottom trace)

Journal: bioRxiv

Article Title: The dynamic response of the bacterial flagellar motor to its direct intracellular input signal

doi: 10.1101/2025.10.28.684865

Figure Lengend Snippet: a . Diagram of key molecules in the chemotaxis network. Extracellular ligands (black semicircles) bind to receptors and modulate the activity of CheA, the kinase that phosphorylates the diffusible messenger CheY. CheA activity adaptation is mediated by the methylase CheR and de-methylase CheB. CheY-P binds to the C-ring and triggers a conformational change that results in BFM changing direction (CCW → CW). The swimming bacterium switches from a smooth run to a tumble. b . AlphaFold structure predictions of chimeric molecules. Grey is E. coli CheY, blue is cpAsLOV2, black is a short linker, and orange is the FliM peptide. Cartoons depicting the “caged” dark-state of Opto-CheY and the constitutively active control are shown with the same color code. c . Blue-light absorption triggers unfolding of the J α helix, and CheY activation by removal of the FliM plug from the CheY active site. Active CheY binds to the C-ring and promotes the rotational switch of the BFM from CCW → CW. Light pulses (blue dots, ~100 µ J/cm 2 ) are applied every 6 seconds while monitoring BFM rotational state. Each response is a CW rotation (vertical black line) following a blue light pulse (blue dot) in an otherwise mostly CCW motor (bottom trace)

Article Snippet: cheY DNA coding sequence was amplified from E. coli genomic DNA; cpAsLOV2 synthesized as a G block by Invitrogen ( ).

Techniques: Chemotaxis Assay, Activity Assay, Control, Activation Assay

Fluorescent signal autocorrelation (black dots) as a function of lag time for a bacterial cell. Data is fitted with a single component diffusion model (red line) with 2 parameters, diffusion time (used to compute the diffusion coefficient) and average number of molecules in the observed volume. Right Scatter plot for the computed upper bound and lower bound concentration for 8 cells (individual cell measurements are shown as gray circles). Mean upper bound is 2.14 ± 0.25 µM and mean lower bound is 1.43 ± 0.17 µM. Assuming the average volume of an E. coli bacterium to be 1 femto-L, each cell contains ~1000-2000 molecules of fluorescent protein.

Journal: bioRxiv

Article Title: The dynamic response of the bacterial flagellar motor to its direct intracellular input signal

doi: 10.1101/2025.10.28.684865

Figure Lengend Snippet: Fluorescent signal autocorrelation (black dots) as a function of lag time for a bacterial cell. Data is fitted with a single component diffusion model (red line) with 2 parameters, diffusion time (used to compute the diffusion coefficient) and average number of molecules in the observed volume. Right Scatter plot for the computed upper bound and lower bound concentration for 8 cells (individual cell measurements are shown as gray circles). Mean upper bound is 2.14 ± 0.25 µM and mean lower bound is 1.43 ± 0.17 µM. Assuming the average volume of an E. coli bacterium to be 1 femto-L, each cell contains ~1000-2000 molecules of fluorescent protein.

Article Snippet: cheY DNA coding sequence was amplified from E. coli genomic DNA; cpAsLOV2 synthesized as a G block by Invitrogen ( ).

Techniques: Diffusion-based Assay, Concentration Assay

Journal: bioRxiv

Article Title: The dynamic response of the bacterial flagellar motor to its direct intracellular input signal

doi: 10.1101/2025.10.28.684865

Figure Lengend Snippet:

Article Snippet: cheY DNA coding sequence was amplified from E. coli genomic DNA; cpAsLOV2 synthesized as a G block by Invitrogen ( ).

Techniques: Transformation Assay, Expressing, Variant Assay

Prevalence of E. coli phylogenetic groups. (A) Prevalence of each phylogenetic group among the total number of clinical isolates analyzed; (B) Prevalence according to the sex of the patient. “?”: Unknown phylogroup.

Journal: Frontiers in Microbiology

Article Title: Comprehensive molecular and phenotypic profiling of uropathogenic Escherichia coli in a Honduran healthcare setting: virulence, resistance and phylogeny

doi: 10.3389/fmicb.2025.1656938

Figure Lengend Snippet: Prevalence of E. coli phylogenetic groups. (A) Prevalence of each phylogenetic group among the total number of clinical isolates analyzed; (B) Prevalence according to the sex of the patient. “?”: Unknown phylogroup.

Article Snippet: Positive controls included DNA from E. coli strains CFT073, ATCC 25922, and UPEC 39, as described in prior publications ( ).

Techniques:

Distribution of the total number of antibiotics to which Escherichia coli isolates are resistant, according to their phylogenetic group. (A) All isolates ( n = 126); (B) Isolates from female patients ( n = 99); (C) Isolates from male patients ( n = 27). In each graph, bars indicate the median and interquartile ranges (IQR).

Journal: Frontiers in Microbiology

Article Title: Comprehensive molecular and phenotypic profiling of uropathogenic Escherichia coli in a Honduran healthcare setting: virulence, resistance and phylogeny

doi: 10.3389/fmicb.2025.1656938

Figure Lengend Snippet: Distribution of the total number of antibiotics to which Escherichia coli isolates are resistant, according to their phylogenetic group. (A) All isolates ( n = 126); (B) Isolates from female patients ( n = 99); (C) Isolates from male patients ( n = 27). In each graph, bars indicate the median and interquartile ranges (IQR).

Article Snippet: Positive controls included DNA from E. coli strains CFT073, ATCC 25922, and UPEC 39, as described in prior publications ( ).

Techniques:

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