Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15435 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1638150.fastq.gz | Fastqsanger.gz | |||
| ERR1638160.fastq.gz | Fastqsanger.gz | |||
| ERR1638151.fastq.gz | Fastqsanger.gz | |||
| ERR1638161.fastq.gz | Fastqsanger.gz | |||
| ERR1638142.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Spring wheat (Triticum aestivum L.) was grown in a free-air carbon dioxide (CO2) enrichment (FACE) field experiment. Grain and biomass yield and its components were determined at maturity and the grain metabolome was analysed by gas chromatography-mass spectrometry (GC-MS) for elevated and ambient CO2 (537 versus 409 μl/l) concentration for samples grown in two successive years (2005, 2006).
2012-09-21 | MTBLS21 | MetaboLights
Project description:Transcriptomic analysis of C. jejuni HPC5 grown in anaerobic jar supplemented with air mix and in Modular Atmospheric Controlled System (MAC). C. jejuni HPC5 is a Campylobacter strain isolated from broiler chickens. Majority of the Campylobacter strains are cultured in an atmosphere containing 5-10% (v/v) oxygen or 5% hydrogen and 5-10% (v/v) carbon dioxide and the rest with nitrogen. To set up a jar (3.5L, Oxoid) to the required microaerophilic conditions, a vacuum is created to -22 psi and then air mixture of 85% v/v nitrogen, 10% v/v carbon dioxide and 5% v/v hydrogen (Air Products, Crewe, UK) is introduced into the jar. This resulted in a microaerobic atmosphere containing approximately 5.6% oxygen, 3.6% hydrogen, 7.3% carbon dioxide and 83% nitrogen. The Modular Atmospheric Controlled System (MAC; Don Whitely Scientific) is an anaerobic chamber where air mixture of 85% nitrogen, 10% carbon dioxide and 5% oxygen is used for growing Campylobacter. Differences in growth pattern were observed when Campylobacters were grown in it and transcriptomic analysis was done to prove the difference in the regulation of genes in the two conditions.
2011-04-01 | GSE17801 | GEO
Project description:Modified atmosphere packaging (MAP) is a common strategy to selectively prevent the growth of certain species of meat spoiling bacteria. While studies on the effectiveness of MAP are still scarce on a putative control over the population of photobacteria detected as meat spoilers, they could develop means to enhance safety and quality of raw meat. This study aims to determine the impact on photobacteria of two modified atmospheres: with high oxygen concentration (red and white meats), and free oxygen MAP (white meats and seafood). We have conducted growth experiments of the two main species found on meat, Photobacterium carnosum (P.) and P. phosphoreum, on a meat simulation media under different gas mixtures of nitrogen, oxygen and carbon dioxide representing air-, high oxygen- and vacuum-like conditions with and without carbon dioxide present. Growth was monitored based on optical density, and samples were taken during exponential growth for a comparative proteomic analysis that allowed the determination of the effects of the different gases and their synergy. Growth under air atmosphere appears optimal particularly for P. carnosum, with enhancement of energy metabolism, respiration, oxygen consuming reactions, and a predicted preference for lipids as carbon source. However, all the other atmospheres show some degree of growth reduction. An increase in oxygen concentration leads to an increase in enzymes counteracting oxidative stress for both species, and enhancement of heme utilization and iron-sulfur cluster assembly proteins for P. phosphoreum. Absence of oxygen appears to switch the metabolism towards fermentative pathways, where either ribose (P. phosphoreum), or glycogen (P. carnosum) appear to be the preferred substrates. Additionally, it promotes the use of alternative electron donors/acceptors, mainly formate and nitrate/nitrite. Stress response is manifested as enhanced expression of enzymes able to produce ammonia (e.g. carbonic anhydrase, hydroxylamine reductase) and regulate osmotic stress. Our results suggest that photobacteria do not sense the environmental levels of carbon dioxide but rather adapt to their own anaerobic metabolism. The regulation in presence of carbon dioxide is limited and strain-specific under anaerobic conditions. However, when oxygen at air-like concentration is present together with carbon dioxide the oxidative stress appears enhanced compared to air conditions (very low carbon dioxide), explained if both gases have a synergistic effect. This is further supported by the increase in oxygen concentration in presence of carbon dioxide. The atmosphere is able to fully inhibit P. carnosum, heavily reduce P. phosphoreum growth in vitro and trigger diversification of energy production with higher energetic cost, highlighting the importance of concomitant bacteria for their growth on raw meat under said atmosphere.
2022-05-31 | PXD031343 | Pride
Project description:The classical bordetellae (Bordetella pertussis, B. parapertussis, and B. bronchiseptica) are obligate aerobes that use only oxygen as their terminal electron acceptor for electron transport-coupled oxidative phosphorylation. Therefore, access to oxygen is critical for these bacteria to survive. To better understand how B. bronchiseptica changes its gene regulation when faced with different levels of oxygen, we grew liquid cultures of B. bronchiseptica RB50 in ambient air, 5% oxygen, and 2% oxygen. We also measured how the presence of 5% carbon dioxide affected gene expression in these bacteria, since they are respiratory pathogens and therefore get exposed to higher carbon dioxide levels during infection than are found in ambient air.
2024-06-07 | GSE268598 | GEO
Project description:Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Several previous transcript-profiling experiments have compared separate anaerobic and aerobic cultures. Here, for the first time, the process of adaptation was investigated by determining changes in transcript profiles when anaerobic steady-state cultures were perturbed by the introduction of air. Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 400 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (30 mM) as the carbon source with the dilution rate being 0.2 h-1. Anaerobic cultures were maintained by sparging the chemostat with oxygen-free nitrogen (95 %) and carbon dioxide (5 %) (0.2 l min-1). The switch to aerobic conditions was achieved by sparging the culture with air (2.0 l min-1) in place of the above gas mix. After a period of 5, 10, 15 and 60 min exposure to air, cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Keywords: time course response to air
2006-07-28 | GSE4735 | GEO
Project description:Transcriptomic analysis of C. jejuni HPC5 grown in anaerobic jar supplemented with air mix and in Modular Atmospheric Controlled System (MAC). C. jejuni HPC5 is a Campylobacter strain isolated from broiler chickens. Majority of the Campylobacter strains are cultured in an atmosphere containing 5-10% (v/v) oxygen or 5% hydrogen and 5-10% (v/v) carbon dioxide and the rest with nitrogen. To set up a jar (3.5L, Oxoid) to the required microaerophilic conditions, a vacuum is created to -22 psi and then air mixture of 85% v/v nitrogen, 10% v/v carbon dioxide and 5% v/v hydrogen (Air Products, Crewe, UK) is introduced into the jar. This resulted in a microaerobic atmosphere containing approximately 5.6% oxygen, 3.6% hydrogen, 7.3% carbon dioxide and 83% nitrogen. The Modular Atmospheric Controlled System (MAC; Don Whitely Scientific) is an anaerobic chamber where air mixture of 85% nitrogen, 10% carbon dioxide and 5% oxygen is used for growing Campylobacter. Differences in growth pattern were observed when Campylobacters were grown in it and transcriptomic analysis was done to prove the difference in the regulation of genes in the two conditions. There are three biological replicates for each experiment. Seven independent cDNA preps of C. jejuni HPC5 were prepared and they were labelled independently using AF555 (Fisher, UK). The labelled cDNAs were mixed together and this acted as the control. C. jejuni HPC5 was grown both in the Jar and in the MAC and their cDNAs were labelled independently with AF645 (Fisher, UK). Hybridisations were done between C. jejuni HPC5 grown in jar and in MAC in triplicates. The supplementary file (linked at the foot of this record) represents the averaged normalised values for each experimental condition (3replicates/experimental condition).
2011-04-01 | E-GEOD-17801 | biostudies-arrayexpress
Project description:RNA sequencing of dissected left atrial free wall and left atrial appendage of adult New Zealand White rabbit
2018-10-19 | GSE117801 | GEO
Project description:Colonoscopy is commonly used in screening for colorectal cancer. A refined technique of colonoscopy involving the use of water as the sole modality to aid colonoscope insertion, water exchange, has been described in recent research papers to decrease patient discomfort and pain, and to reduce the need for sedation during colonoscopy when compared with standard air insufflation. Carbon dioxide insufflation has been described to decrease patient discomfort after colonoscopy. No randomized trial has so far compared the use of water exchange to carbon dioxide insufflation. Our hypothesis is that water exchange inflicts less discomfort to patients undergoing colonoscopy than carbon dioxide insufflation. Patients undergoing screening colonoscopy in two centers in Norway, one center in Poland and one center in The Netherlands will be enrolled and randomized to examination of either of the two methods.
| 2128017 | ecrin-mdr-crc
Project description:Our goal was to investigate the transcriptomes changes on rats liver, brain, thymus, and spleen after exposure to an indoor school air mixture (SAM+) of polychlorinated biphenyls (PCBs). Female Sprague-Dawley rats were exposed to SAM+ at a concentration of 45.5±5.9 µg/m^3 Σ209PCB or filtered air (sham group) 4 h/day, 6 days/week for 13 weeks using nose-only exposure systems. Twenty-four hours after the final exposure, rats were euthanized by carbon dioxide inhalation followed by cervical dislocation. Cardiac blood was collected and organs were excised and stored at -80 °C until analysis.
2021-06-30 | GSE179117 | GEO
Project description:Land cover change has long been recognized that marked effect the amount of soil organic carbon. However, little is known about microbial-mediated effect processes and mechanism on soil organic carbon. In this study, the soil samples in a degenerated succession from alpine meadow to alpine steppe meadow in Qinghai-Tibetan Plateau degenerated, were analyzed by using GeoChip functional gene arrays.
2017-01-05 | GSE93158 | GEO