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E-TABM-912
Escherichia coli
48 Downloadable Samples
Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
The foodborne pathogen Escherichia coli O157:H7 is commonly exposed to organic acid in processed and preserved foods, allowing adaptation and the development of tolerance to pH levels otherwise lethal. Since little is known about the molecular basis of adaptation of E. coli to organic acids, we studied K-12 MG1655 and O157:H7 Sakai during exposure to acetic-, lactic-, and hydrochloric acid at pH 5.5. The conditions required to maximimally induce the ATR of the pathotypes to all acidulants was experimentally determined. This involved incubation at pH 5.5 for 3 h (K-12) and for 2 h (O157:H7), and generated acid adapted cultures more resistant to acid challenge at pH 3.5 than bacteria that had been grown at neutral pH prior to acid-shock. To determine the transcriptomic response of K-12 and O157:H7 to each of the three acids, RNA was extracted from samples of cultures at the time of incubation corresponding to maximal induction of the ATR and from the corresponding overnight culture to serve as a control. The Affy package of the Bioconductor software was used to process raw CEL files using the robust multiarray average algorithm (RMA) for normalization, background correction, and expression value calculation. Expression levels obtained from four independent biological replicates of every condition were compared using the Limma package of the Bioconductor software. Elements with expression levels ? twofold higher or lower than the reference at a statistical significance (P-value adjustment with Benjamini and Hochberg with an adjusted P value ? 0.01, Average Expression (A value) ? 2, Log-odds (B value) ? 0) were selected. This is the first transcriptomic study to demonstrate and characterise the stationary phase acidulant and pathotype specific ATR of E. coli. A core set of genes were also found to be universally expressed by both pathotypes regardless of acidulant type.
Publication Title
Transcriptomic analysis of the acid tolerance responses of Escherichia coli O157:H7 and K-12 to inorganic and organic acids reveals an acidulant and pathotype-specific response
Sample Metadata Fields
Subject, Compound, Time
View Samples- Escherichia coli
- 15 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
In a previous study we adopted an integrated transcriptomic and proteomic approach to determine the physiological response of E. coli O157:H7 Sakai during exponential phase growth under steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcass chilling in cold air (Kocharunchitt et al., 2012). The findings of that study provide a baseline of knowledge of the physiology of this pathogen, with the response of E. coli O157:H7 to steady-state conditions of combined cold and osmotic stress. To provide an insight into the genetic systems enabling this organism to adapt to growth at low temperature, we extended the aforementioned study to investigate the growth kinetics of E. coli O157:H7 Sakai during abrupt temperature downshift from 35 degrees C to 14 degrees C and, examined time-dependent global alterations in its genome expression upon cold shock from 35 degrees C to 14 degrees C. The genome-wide expression response of E. coli was analysed by both cDNA microarray (transcriptome response) and 2D-LC/MS/MS analysis (proteome response). Differences in gene and protein expression patterns in E. coli before and after cold shock were analysed through quantitative and comparative analysis of time series changes in both mRNA and proteins levels.
Publication Title
Global genome response of Escherichia coli O157:H7 Sakai during dynamic changes in growth kinetics induced by an abrupt temperature downshift
Sample Metadata Fields
Time
View Samples- Escherichia coli
- 15 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
An integrated genomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcase chilling in cold air. The response of E. coli during exponential growth at 25°C aw 0.985, 14°C aw 0.985, 25°C aw 0.967 and, 14°C aw 0.967 was compared to that of a reference culture (35°C aw 0.993).
Publication Title
Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress
Sample Metadata Fields
Subject
View Samples- Arabidopsis thaliana
- 7 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global analysis of brassinosteroid (BR)-mediated gene expression under abiotic stress identifies BR associated mechanisms of stress tolerance, and new stress-related genes
Publication Title
Gene expression and functional analyses in brassinosteroid-mediated stress tolerance.
Sample Metadata Fields
Age, Specimen part
View Samples- Vitis vinifera
- 174 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models.
Sample Metadata Fields
No sample metadata fields
View Samples- Vitis vinifera
- 68 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Changes in gene expression during berry development during a grape growing season were analysed. The effect on gene expression of different viticultural practises during grape berry development was investigated in this study by comparing two irrigation methods (standard versus prolonged deficit irrigation).
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Vitis vinifera
- 68 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Changes in gene expression during berry development during a grape growing season were analysed. The effect on gene expression of different viticultural practises during grape berry development was investigated in this study by comparing two pruning methods (spur versus machine).
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 47 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
ZnO and TiO2 nanoparticles can elicit a range of perturbed cell responses in vitro. Exposure to topically applied sunscreens containing ZnO or TiO2 particles may or may not elicit a biological effect in mice. We aimed to compare the biological responses of immune-competent hairless mice receiving topical applications of commercially available sunscreens with or without metal oxide nanoparticles, with the responses of mice receiving no sunscreen.
Publication Title
Long-term exposure to commercially available sunscreens containing nanoparticles of TiO2 and ZnO revealed no biological impact in a hairless mouse model.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 46 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
ZnO nanoparticles can elicit a range of perturbed cell responses in vitro. Exposure to topically applied sunscreens containing ZnO particles may or may not elicit a biological effect in mice.
Publication Title
Dermal absorption and short-term biological impact in hairless mice from sunscreens containing zinc oxide nano- or larger particles.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 43 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples