Ontology highlight
ABSTRACT:
PROVIDER: PRJNA945084 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23877600_1.fastq.gz | Fastqsanger.gz | |||
| SRR23877600_2.fastq.gz | Fastqsanger.gz | |||
| SRR23877601_1.fastq.gz | Fastqsanger.gz | |||
| SRR23877601_2.fastq.gz | Fastqsanger.gz | |||
| SRR23877602_1.fastq.gz | Fastqsanger.gz |
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Project description:Three surface waters in Gainesville, Florida were used in a 48 hour whole effluents exposure to assess gene expression profiles of male fathead minnow liver. Microarray analysis was used to determine changes in gene expression of exposed fish to waters from a site downstream of a wastewater treatment plant (streamwater), a wastewater treatment plant (wastewater), and a lake (stormwater). Differences in gene expression between fish exposed to collected waters and controls were observed. Number of altered genes and biological processes were 1028 and 18 for stormwater; 787 and 19 for streamwater; and: 575 and 12 for wastewater. In general, the effects observed in all exposed fish were related with fatty acid metabolism, DNA repair, oxidation-reduction process, cell wall catabolic process and apoptosis. All exposed fish showed altered expression of genes related with DNA damage repair. In particular fish exposed to stormwater and streamwater showed downregulation of several key intermediates transcripts of cholesterol. The presence and environmental persistence of perfluorinated chemicals (PFCs) in these waters, the resemblance in known effects on transcripts with those found in this study, suggest that the set of genes differentially regulated in fathead minnows after 48 hours of exposure may be attributed to exposure to PFCs. Three surface water sites were chosen for effluent collection in Gainesville, Florida: A lake (stormwater), surface water downstream of a wastewater treatment plant (streamwater), and a wastewater treatment plant effluent used for landscaping irrigation (wastewater). Water from each site was collected two days prior to the fish exposure experiment using Chemfluor ® tubing and a 120 liters steel barrels coated with polyester resin (gel coat) to avoid cross-contamination. Three barrels for each effluent were collected during day 1. Water from the barrel was transported to the laboratory and pumped into four fiberglass cylinders in the aquatic toxicology facility. Water from each cylinder was then pumped into four replicate aquariums per treatment and kept for 1 day without fish (pre-treatment). On day 2, four male fathead minnows from a common tank were transferred to each replicate aquarium and kept for 48 hours, with one 75% water change after first 24 hours. The exposure system consisted of 40 L glass aquaria. Each exposure was conducted in quadruplicate and each aquarium contained the four male fish in 25 L of treatment water . The water used in the control treatment was carbon filtered, dechlorinated tap water. The positions of the treatment tanks were randomized and test initiation times were staggered to ensure an exposure/sampling interval of 48 h. The fish were not fed during the experiment. The temperature range of the water was 24-26 °C with a photoperiod of 16 h light: 8 h dark. Liver was isolate from 4 males indviduals for each treatment except for control group (3 individuals).
2012-04-24 | E-GEOD-37550 | biostudies-arrayexpress
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level. Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source
2012-07-31 | E-GEOD-39065 | biostudies-arrayexpress
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level.
2012-08-01 | GSE39065 | GEO
Project description:As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation by the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutation in the gene encoding the cyclic AMP receptor protein, Crp*, has been shown to disable CCR and improve co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site specific crp* chromosomal mutant in E. coli BL21 starTM (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomic analysis further showed that cells link xylose consumption to energy production through the de novo nucleotide synthesis pathway, explaining the relatively slower growth of the crp* mutant strain. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.
| MSV000092810 | MassIVE
Project description:Bio-augmentation could be a promising strategy to improve processes for treatment and resource recovery from wastewater. In this study, the Gram-positive bacterium Bacillus subtilis was co-cultured with the microbial communities present in wastewater samples with high concentrations of nitrate or ammonium. Glucose supplementation (1%) was used to boost biomass growth in all wastewater samples. In anaerobic conditions, the indigenous microbial community bio-augmented with B. subtilis was able to rapidly remove nitrate from wastewater. In these conditions, B. subtilis overexpressed nitrogen assimilatory and respiratory genes including NasD, NasE, NarG, NarH, and NarI, which arguably accounted for the observed boost in denitrification. Next, we attempted to use the the ammonium- and nitrate-enriched wastewater samples bio-augmented with B. subtilis in the cathodic compartment of bioelectrochemical systems (BES) operated in anaerobic condition. B. subtilis only had low relative abundance in the microbial community, but bio-augmentation promoted the growth of Clostridium butyricum and C. beijerinckii, which became the dominant species. Both bio-augmentation with B. subtilis and electrical current from the cathode in the BES promoted butyrate production during fermentation of glucose. A concentration of 3.4 g/L butyrate was reached with a combination of cathodic current and bio-augmentation in ammonium-enriched wastewater. With nitrate-enriched wastewater, the BES effectively removed nitrate reaching 3.2 mg/L after 48 h. In addition, 3.9 g/L butyrate was produced. We propose that bio-augmentation of wastewater with B. subtilis in combination with bioelectrochemical processes could both boost denitrification in nitrate-containing wastewater and enable commercial production of butyrate from carbohydrate- containing wastewater, e.g. dairy industry discharges. These results suggest that B. subtilis bio-augmentation in our BES promotes simultaneous wastewater treatment and butyrate production.
2020-05-15 | GSE150480 | GEO
Project description:Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes. This project contains datasets derived from the same biological wastewater treatment plant. The data includes metagenomes, metatranscriptomes, metaproteomes and organisms isolated in pure cultures. Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes. This project contains datasets derived from the same biological wastewater treatment plant. The data includes metagenomes, metatranscriptomes, metaproteomes and organisms isolated in pure cultures.
2020-08-19 | PXD013655 | Pride
Project description:Understanding microbial community diversity is thought to be crucial for improving process functioning and stabilities of wastewater treatment systems. However, current studies largely focus on taxonomic groups based on 16S rRNA, which are not necessarily linked to functioning, or a few selected functional genes. Here we launched a study to profile the overall functional genes of microbial communities in three full-scale wastewater treatment systems. Triplicate activated sludge samples from each system were analyzed using a high-throughput metagenomics tool named GeoChip 4.2, resulting in the detection of 38,507 to 40,647 functional genes. A high similarity of 75.5% to 79.7% shared genes was noted among the nine samples. Moreover, correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of overall nitrogen cycling genes had a strong correlation to total nitrogen (TN) removal rates (r = 0.7647, P < 0.01). The abundances of overall carbon cycling genes were moderately correlated with COD removal rates (r = 0.6515, P < 0.01). Lastly, we found that influent chemical oxygen demand (COD inf) and total phosphorus concentrations (TP inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.
2014-12-31 | GSE53744 | GEO