Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR33653736_1.fastq.gz | Fastqsanger.gz | |||
| SRR33653736_2.fastq.gz | Fastqsanger.gz | |||
| SRR33653738_1.fastq.gz | Fastqsanger.gz | |||
| SRR33653738_2.fastq.gz | Fastqsanger.gz |
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Project description:A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. This method allows the detection and discrimination of single bacterial species in a complex sample. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non-growing bacteria. The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage microorganisms within mixed population. Keywords: microarray, oligonucleotide, species-specific, detection, beer spoilage bacteria
2007-05-23 | GSE7840 | GEO
Project description:Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria
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Project description:The yeast Dekkera bruxellensis is as ethanol tolerant as Saccharomyces cerevisiae and may be found in bottled wine. It causes the spoilage of wine, beer, cider and soft drinks. In wines, the metabolic products responsible for spoilage by Dekkera bruxellensis are mainly volatile phenols. These chemical compounds are responsible for the taints described as ‘‘medicinal’’ in white wines (due to vinyl phenols) and as ‘‘leather’’, ‘‘horse sweat’’ and ‘‘stable’’ in red wines (due to ethyl phenols mainly 4-ethylphenol). Apart from the negative aroma nuances imparted by these yeasts, positive aromas such as ‘smoky’, ‘spicy’ and ‘toffee’ are also cited. Our goal was to identify the impact that the wine spoilage yeast Dekkera bruxellensis has on fermenting S. cerevisiae cells, especially on its gene expression level. To this end we co-inoculated both yeast species at the start of fermentation in a synthetic wine must, using S. cerevisiae-only fermentations without Dekkera bruxellensis as a control. All fermentations were employed in special membrane reactors (1.2 um pore size cut-off) physically separating Dekkera bruxellensis from wine yeast S. cerevisiae. Biomass separation with this membrane was done to abolish the possibility of hybridizing also D. bruxellensis probes on Agilent V2 (8x15K format) G4813 DNA microarrays designed just for S. cerevisiae ORF targets. The 1.2 um pore membrane separating both yeasts allowed the exchange of ethanol, metabolites and sugars during the fermentation.
2012-06-13 | GSE38582 | GEO
Project description:The yeast Dekkera bruxellensis is as ethanol tolerant as Saccharomyces cerevisiae and may be found in bottled wine. It causes the spoilage of wine, beer, cider and soft drinks. In wines, the metabolic products responsible for spoilage by Dekkera bruxellensis are mainly volatile phenols. These chemical compounds are responsible for the taints described as M-bM-^@M-^XM-bM-^@M-^XmedicinalM-bM-^@M-^YM-bM-^@M-^Y in white wines (due to vinyl phenols) and as M-bM-^@M-^XM-bM-^@M-^XleatherM-bM-^@M-^YM-bM-^@M-^Y, M-bM-^@M-^XM-bM-^@M-^Xhorse sweatM-bM-^@M-^YM-bM-^@M-^Y and M-bM-^@M-^XM-bM-^@M-^XstableM-bM-^@M-^YM-bM-^@M-^Y in red wines (due to ethyl phenols mainly 4-ethylphenol). Apart from the negative aroma nuances imparted by these yeasts, positive aromas such as M-bM-^@M-^XsmokyM-bM-^@M-^Y, M-bM-^@M-^XspicyM-bM-^@M-^Y and M-bM-^@M-^XtoffeeM-bM-^@M-^Y are also cited. Our goal was to identify the impact that the wine spoilage yeast Dekkera bruxellensis has on fermenting S. cerevisiae cells, especially on its gene expression level. To this end we co-inoculated both yeast species at the start of fermentation in a synthetic wine must, using S. cerevisiae-only fermentations without Dekkera bruxellensis as a control. All fermentations were employed in special membrane reactors (50 KDa pore size cut-off) physically separating Dekkera bruxellensis from wine yeast S. cerevisiae. Biomass separation with this membrane was done to abolish the possibility of hybridizing also D. bruxellensis probes on Agilent V2 (8x15K format) G4813 DNA microarrays designed just for S. cerevisiae ORF targets. The 50 KDa pore membrane separating both yeasts allowed the exchange of ethanol, metabolites and sugars during the fermentation. Fermentations were carried out in synthetic wine must in duplicate for both the control S. cerevisiae (strain Lalvin EC1118) and mixed fermentation. Sampling of yeast S. cerevisiae for RNA extractions were performed at 22 h of fermentation, during the exponential growth phase of S. cerevisiae, at 92 h and 144 h of fermentation, during its early and late stationary growth phase and at 187 h of fermentation, during its phase of growth decline.
2012-06-12 | E-GEOD-38582 | biostudies-arrayexpress
Project description:Aiming to reduce food spoilage, the present study developed novel highly active food-grade preservatives affecting a wide range of bacteria. For this purpose, storage proteins were extracted from food plants. After enzymatic hydrolysis by the digestive protease chymotrypsin, the peptide profiles were analyzed by ultrahigh-performance micro-liquid chromatography–triple quadrupole time-of-flight tandem mass spectrometry. Virtual screening identified 21 potential antimicrobial peptides in chickpea legumin. Among those, the peptides Leg1 (RIKTVTSFDLPALRFLKL) and Leg2 (RIKTVTSFDLPALRWLKL) exhibited antimicrobial activity against 16 different bacteria, including pathogens, spoilage-causing bacteria and two antibiotic-resistant strains. Minimum inhibitory concentrations (MIC) down to 15.6 µM indicated 10–1,000-fold higher activity of the novel antimicrobial peptides compared to conventional food preservatives. Moreover, Leg1 and Leg2 showed bactericidal activity in bacterial suspension and during the storage of raw pork meat.
2021-01-11 | PXD019257 | Pride