Determination of Survival of Wildtype and Mutant Escherichia coli in Soil

Somorin, Yinka; O’Byrne, Conor

doi:10.21769/bioprotoc.2414

Cited by 4 publications

(3 citation statements)

References 12 publications

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“…RpoS is the master regulator of the general stress response in E. coli and essential for survival under a variety of stress conditions (Hengge, 2009). The importance of a functional RpoS for long‐term soil survival of E. coli has also been shown by other authors (Somorin et al, 2016, 2017; Somorin & O'Byrne, 2017). The authors demonstrated that the rpoS gene is highly conserved in long‐term soil persistent E. coli strains and that RpoS is essential for protecting the bacteria against unfavourable conditions such as low pH or reduced moisture which are present in soils.…”

Section: Discussionsupporting

confidence: 69%

Broad time‐dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

Detert,

Währer,

Nieselt

et al. 2023

Environ Microbiol Rep

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In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

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Section: Discussionsupporting

confidence: 69%

Broad time‐dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

Detert,

Währer,

Nieselt

et al. 2023

Environ Microbiol Rep

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show abstract

“…The reading of OD at 600 nm was determined through UV-VIS spectrophotometry (E-Chrom Tech) to estimate the cell density of bacteria. An OD at 600 nm corresponds to 2 × 10 8 cells/mL [25]. Plasmid DNA was extracted from this bacterial culture using a QIAGEN Plasmid Maxi Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer's instructions and dissolved in sterilized deionized-distilled water.…”

Section: Bacterial Culture and Nucleic Acid Extractionmentioning

confidence: 99%

Development of a Nucleic Acid Lateral Flow Immunoassay for the Detection of Human Polyomavirus BK

Huang

et al. 2020

Diagnostics

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The BK virus (BKV) is an emerging pathogen in immunocompromised individuals and widespread in the human population. Polymerase chain reaction is a simple and highly sensitive method for detecting BKV, but it is time consuming and requires expensive instruments and expert judgment. The lateral flow assay, a rapid, low-cost, minimal-labor, and easy-to-use diagnostic method, was successfully applied for pathogen detection. In this study, we used oligonucleotide probes to develop a simple and rapid sandwich-type lateral flow immunoassay for detecting BKV DNA within 45 minutes. The detection limit for the synthetic single-stranded DNA was 5 nM. The specificity study showed no cross-reactivity with other polyomaviruses, such as JC virus and simian virus 40. For the Escherichia coli containing BKV plasmid cultured samples, the sensitivity was determined to be 107 copies/mL. The approach offers great potential for BKV detection of various target analytes in point-of-care settings.

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“…For E. blattae, we constructed a calibration curve of cell concentration versus OD 600 , based on a protocol by Somorin and O'Byrne. 25)…”

Section: Bacteria Culturing and Quantificationmentioning

confidence: 99%

An imaging study and spectroscopic curing analysis on polymers for synthetic whole-cell receptors for bacterial detection

Givanoudi

Gennaro

Yongabi

et al. 2020

Jpn. J. Appl. Phys.

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Surface imprinted polymers (SIPs) are versatile receptors in bioanalytical applications for the selective detection of cells and microorganisms such as bacteria. One of the synthesis routes is the so-called stamping method in which template bacteria are pressed mechanically into a thin, gel-like polyurethane layer, which is then cured in the presence of the templates to create cell-specific binding pockets on the polymer. The present work focusses on two specific steps of the imprinting protocol: first, we evaluate the sedimentation of two different groups of bacteria, Escherichia coli and Escherichia blattae, on silicone stamps with respect to the resulting surface coverage, which is a key factor for the efficiency of the imprinting process. Second, we analyse the temperature dependence of the thermal- and dielectric properties of polyurethane during curing by dielectric- and pyroelectric spectroscopy. This provides information for improved curing protocols and on the stability of SIP materials at elevated temperatures.

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Determination of Survival of Wildtype and Mutant Escherichia coli in Soil

Cited by 4 publications

References 12 publications

Broad time‐dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

Broad time‐dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

Development of a Nucleic Acid Lateral Flow Immunoassay for the Detection of Human Polyomavirus BK

An imaging study and spectroscopic curing analysis on polymers for synthetic whole-cell receptors for bacterial detection

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