Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1041065 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26846700_1.fastq.gz | Fastqsanger.gz | |||
| SRR26846700_2.fastq.gz | Fastqsanger.gz | |||
| SRR26846701_1.fastq.gz | Fastqsanger.gz | |||
| SRR26846701_2.fastq.gz | Fastqsanger.gz | |||
| SRR26846702_1.fastq.gz | Fastqsanger.gz |
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Project description:Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures. To maximize PHA production, mixed microbial cultures may be enriched for PHA-producing bacteria with a high storage capacity through the imposition of cyclic, aerobic feast-famine conditions in a sequencing batch reactor (SBR). Though enrichment SBRs have been extensively investigated a bulk solutions-level, little evidence at the proteome level is available to describe the observed SBR behavior to guide future SBR optimization strategies. As such, the purpose of this investigation was to characterize proteome dynamics of a mixed microbial culture in an SBR operated under aerobic feast-famine conditions using fermented dairy manure as the feedstock for PHA production. At the beginning of the SBR cycle, excess PHA precursors were provided to the mixed microbial culture (i.e., feast), after which followed a long duration devoid of exogenous substrate (i.e., famine). Two-dimensional electrophoresis was used to separate protein mixtures during a complete SBR cycle, and proteins of interest were identified.
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Project description:transcriptomics of feast-famine reactors
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Project description:In nature, animals often face feast or famine conditions. We aimed to identify the miRNAs of Caenorhabditis elegans that changed their expression under starvation conditions in stage L4 larvae. Our results highlight 14 miRNAs that show differential expression in starved versus well-fed larvae. In particular, miRNAs of the miR-35-3p/miR-41-3p family were upregulated 6-20 fold upon starvation. We verified the upregulation of miR-35-3p with qPCR. Additionally, we showed that the expression of gld-1, important in ovogenesis, and a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was higher. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans.
2016-01-27 | GSE67711 | GEO
Project description:In nature, animals often face feast or famine conditions. We aimed to identify the miRNAs of Caenorhabditis elegans that changed their expression under starvation conditions in stage L4 larvae. Our results highlight 14 miRNAs that show differential expression in starved versus well-fed larvae. In particular, miRNAs of the miR-35-3p/miR-41-3p family were upregulated 6-20 fold upon starvation. We verified the upregulation of miR-35-3p with qPCR. Additionally, we showed that the expression of gld-1, important in ovogenesis, and a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was higher. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans. Illumina small RNA sequencing of starved and well-fed L4 worms.
2016-01-27 | E-GEOD-67711 | biostudies-arrayexpress
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Project description:Background. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continiouslly fed biofilm reactor, and compared to both batch and reactor planktonic populations. The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenases as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion. Biofilms grown in reactors were compared to reference samples of reactor, planktonic and batch, planktonic. Each sample had a biological triplicate.
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