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PROVIDER: PRJNA1020663 | ENA |
REPOSITORIES: ENA
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Project description:The physiological and transcriptional response of Nitrosomonas europaea biofilms to phenol and toluene was examined and compared to suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors under continuous flow conditions of growth medium containing ammonia as growth substrate. The responses of N. europaea biofilms to the aromatic hydrocarbons phenol and toluene were determined during short-term (3 h) additions of each compound to the biofilms. Ammonia oxidation in the biofilms was inhibited 50% by 60 uM phenol and 100 uM toluene. These concentrations were chosen for microarray analysis of phenol- and toluene-exposed N. europaea biofilms. Liquid batch cultures of exponentially growing N. europaea cells were harvested alongside the biofilms to determine differential gene expression between attached and suspended growth of N. europaea. Four sample groups of N. europaea cells were used in this study, with biological triplicates of each group. Groups were: Control (untreated) biofilms, phenol-exposed biofilms, toluene-exposed biofilms, and exponentially growing suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors containing 4 independent growth channels and subject to 2 hour inhibition tests. During each experiment, 2 biofilm channels served as control with no inhibitor present and the other 2 biofilm channels were exposed to either 60 uM phenol or 100 uM toluene. Nitrite production was monitored throughout the experiment, and the given concentrations of phenol and toluene resulted in 50% inhibition of ammonia oxidation by the biofilms. Suspended cells were grown in batch reactors. Three 4-plex NimbleGen microarray chips were used, and each chip contained one sample from each experimental group. QC of samples was determined by spectrophotometric methods and using Agilent bioanalyzer traces to determine purity and integrity of RNA and cDNA. A sample tracking report was used to verify the correct hybridization of each sample to the intended array.
2010-07-20 | E-GEOD-22646 | biostudies-arrayexpress
Project description:Native mass spectrometry (MS) has become an important technique in several fields including structural biology and drug discovery, due to its ability to study non-covalent assemblies in the gas phase. In many settings, the main drawbacks of native MS are the incompatibility of electrospray ionisation with non-volatile salts and the risk of protein signal suppression if small, efficiently ionising molecules are present in the sample. This often requires an offline buffer exchange step and/or parallel sample preparation workflow to other analytical methods, reducing both the adoption and the throughput of native MS. Here, we exploit the dynamics of analytes flowing through an open tubular capillary to keep molecules with a small hydrodynamic radius (e.g., salts) inside a Taylor dispersion regime, while pushing larger species (e.g., proteins) into a non-Taylor regime. The result of this is that the larger species elute earlier, and are effectively buffer exchanged within the capillary on a timescale of approximately 30 seconds. In addition to desalting of proteins injected in solutions containing 25 to 200 mM NaCl and other biologically relevant buffers (e.g., HEPES, TCEP, and glycerol), we also demonstrate that this method can separate unbound small molecules from protein-ligand complexes, enabling rapid, multiplexed ligand screening based on native MS. Finally, we investigated the dependence of the critical flow rate required to push proteins outside the Taylor regime on protein size, enabling limited size-based separation of proteins and providing a starting point for others to adopt this method. Taylor/non-Taylor dispersion mass spectrometry (TNT-MS) was implemented using an unmodified LC-MS system operated without a chromatographic column and coupled to an autosampler. This allows significant automation, which we believe will contribute to the wider adoption of native MS as a routine method.
2025-07-10 | PXD063440 | Pride
Project description:Investigating certain gene expressions in the VOC pathway and in lactate signaling, parallel to VOC production.
2025-03-23 | GSE228336 | GEO
Project description:Abstract: Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared rankings for a priori identified physiological marker genes between the biofilm and published data sets. Two drip flow biofilm conditions with three replicates each: (1) baseline control at 72hrs, (2) no treatment for 12 hours past baseline. Data from these two conditions were pooled
2010-11-20 | E-GEOD-22164 | biostudies-arrayexpress
Project description:In this study a gene expression (i.e., RNAseq) analysis was performed in HEK293T-ACE2 cellular model upon infection with viral particle belonging to VOC Delta (MOI: 0.026) for 24 hours in order to have a global picture of the transcriptome landscape in response to early phase of infection of SARS-CoV-2 ( VOC Delta infection and to evaluate the role of Ca2+ in HEK293-ACE2 cellular model and transfer to homeostasis in SARS-COV-2 patients (by Pasqualino de Antonellis1-2* and Veronica Ferrucci 1-2* (first authors) et al. and Massimo Zollo1-2# (corresponding author). Manuscript in preparation 2022 July 15th 2022. Short title "ATP2B1 (PMCA1), regulated by FOXO3, influences susceptibility to severe COVID19".
2022-12-01 | E-MTAB-11973 | biostudies-arrayexpress
Project description:Abstract: Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared rankings for a priori identified physiological marker genes between the biofilm and published data sets.
2010-11-20 | GSE22164 | GEO
Project description:Purpose: RNA-Seq was performed for gene expression analysis following infection of human cells with different VOC depending on the experiment group to investigate changes in the host and viral molecular response. Methods: RNA was extracted from 10^6 cells using the Qiagen RNeasy extraction kit according to the manufacturer's protocol and quantified by nanodrop. Samples were submitted for RNA-Seq to Genewiz (Azenta) for library preparation and subsequent steps. Results: We have identified SARS-CoV-2 VOC-specific differences in RNA expression, including for N, Orf9b, and Orf6. We have also measured ISG expression and proinflammatory gene suppression across the VOC, determining changes in ISG expression and proinflammatory gene suppression during amongst VOC during SARS-CoV-2 evolution. Conclusions: Our study examines changes in the host molecular response to VOC infection to identify changes in gene expression, especially those related to the innate immune response, that have occurred during SARS-CoV-2 evolution.
2023-09-20 | GSE213759 | GEO