Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA964711 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Repeatable growth of tree hole bacterial communities in the laboratory
| PRJNA989519 | ENA
Project description:The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An intricately choreographed expression program devoted to communication between cells was a prominent feature of the response. Other features suggested a molecular program for commitment of antigen-presenting cells to antigens captured in the context of bacterial infection. Despite the striking similarities, there were qualitative and quantitative differences in the responses to different bacteria. Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-11-16 | GSE3611 | GEO
Project description:The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An intricately choreographed expression program devoted to communication between cells was a prominent feature of the response. Other features suggested a molecular program for commitment of antigen-presenting cells to antigens captured in the context of bacterial infection. Despite the striking similarities, there were qualitative and quantitative differences in the responses to different bacteria. Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Using regression correlation
2005-11-15 | E-GEOD-3611 | biostudies-arrayexpress
Project description:Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers.
2014-12-03 | GSE63781 | GEO
Project description:Pea plants of 7, 14 or 21 were infected with Rhizobium leguminosarum biovar viciae strain Rlv3841 and bacterial gene expression measured 24 hours later. Expression was compared to bacteria grown in the laboratory on glucose ammonia.
2010-10-01 | E-MEXP-2845 | biostudies-arrayexpress
Project description:Under well-defined laboratory conditions, we grew R. pomeroyi DSS-3 and A. macleodii MIT1002 in batch cultures on a monosaccharide (glucose) and organic acid (acetate), provided either individually or in combination, and all at the same carbon equivalent. This batch culturing approach mimicked bacterial DOC assimilation in short-lived substrate ‘hot spots’, such as those formed by high phytoplankton extracellular release at peak photon availability. Measurements were made of bacterial metabolite uptake, respiration, and biomass accumulation through a growth cycle. Insights into bacterial core metabolism came from gene and protein expression measured at intervals during growth. Curated genome-scale models (flux balance analysis; FBA) were used to explore the metabolic foundation of CO2 production for insights into determinants of BGE and bCUE.
2023-10-27 | PXD045824 | Pride
Project description:Genome sequencing and assembly - library of cultured bacterial species from laboratory mouse gut microbiota from the University of Toronto
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Project description:Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based, transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH, a method enabling high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of B. thetaiotaomicron to micron-scale niches in the mammalian colon. We envision bacterial-MERFISH could prove useful in the study of bacterial single-cell decisions made in diverse, spatially structured, and native environments.
2024-11-12 | GSE268480 | GEO