Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pseudomonas pseudoalcaligenes CECT5344 response to cyanide vs. ammonium or nitrogen starvation

ABSTRACT: Transcriptional analysis of the cyanotroph Pseudomonas pseudoalcaligenes CECT5344 in response to cyanide present in wastewaters from industrial activities, such as jewelry and electroplating activities Four-conditions experiment, including three different nitrogen sources (ammonium, sodium cyanide or a cyanide-containing wastewater). One experiment without nitrogen added to the media (nitrogen limited condition). Four biological replicates for each condition (added nitrogen source to the media) plus the experiment without nitrogen source added.

ORGANISM(S): Pseudomonas pseudoalcaligenes CECT 5344

SUBMITTER: Victor M. Luque

PROVIDER: E-GEOD-69930 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

DNA microarray analysis of the cyanotroph Pseudomonas pseudoalcaligenes CECT5344 in response to nitrogen starvation, cyanide and a jewelry wastewater.

Luque-Almagro V M VM Escribano M P MP Manso I I Sáez L P LP Cabello P P Moreno-Vivián C C Roldán M D MD

Journal of biotechnology 20150930

Pseudomonas pseudoalcaligenes CECT5344 is an alkaliphilic bacterium that can use cyanide as nitrogen source for growth, becoming a suitable candidate to be applied in biological treatment of cyanide-containing wastewaters. The assessment of the whole genome sequence of the strain CECT5344 has allowed the generation of DNA microarrays to analyze the response to different nitrogen sources. The mRNA of P. pseudoalcaligenes CECT5344 cells grown under nitrogen limiting conditions showed considerable ...[more]

PMID: 26432339

Similar Datasets

Quantitative proteomic analysis (LC-MS/MS) of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters

Project description:Biological treatments to degrade cyanide have shown to be a powerful technology for cyanide removal from industrial wastewaters. It has been previously demonstrated that the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to use free cyanide and several metal−cyanide complexes as the sole nitrogen source. The strain CECT5344 has been used for detoxification of the different chemical forms of cyanide that are present in alkaline wastewaters from the electroplating process of the jewelry industry. This liquid residue also contains large concentrations of metals like iron, copper and zinc, making this wastewater even more toxic. A proteomic analysis by LC-MS/MS has been applied to elucidate the molecular mechanisms involved in this bioremediation process in P. pseudoalcaligenes CECT5344. Among others, different proteins related to cyanide and cyanate assimilation, as well as other proteins involved in transport and resistance to metals were induced by the cyanide-containing jewelry residue have been identified.

2017-03-08 | PXD005056 | Pride

Utilisation of glucose by Pseudomonas putida KT2440 (PB2440) under nitrogen varying conditions

Project description:The response of P. putida KT2440 (PB2440) to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with 2mM glucose as carbon source and different concentration of ammonium chloride as nitrogen source. For nitrogen limiting condition 2mM ammonium chloride was used whereas, for nitrogen rich condition 20mM ammonium chloride was added in the medium. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.

2014-04-24 | E-MTAB-2536 | biostudies-arrayexpress

Utilisation of phenol by Pseudomonas putida CF600 under nitrogen varying conditions

Project description:The response of P. putida CF600 to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with 2mM phenol as carbon source and different concentration of ammonium chloride as nitrogen source. For nitrogen limiting condition 2mM ammonium chloride was used whereas, for nitrogen rich condition 20mM ammonium chloride was added in the medium. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.

2014-04-24 | E-MTAB-2535 | biostudies-arrayexpress

Utilisation of naphthalene by Pseudomonas putida CSV86 under nitrogen varying conditions

Project description:The response of P. putida CSV86 in response to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with either naphthalene (0.1%) alone or along with glucose (0.25%) as carbon source and different concentration of ammonium nitrate. For nitrogen limiting 0.1% NH4N03 was added in the medium and for nitrogen rich 1% NH4N03 was used. As control CSV86 was also grown in 1X Luria Broth with glucose as additional carbon source. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.

2014-04-24 | E-MTAB-2528 | biostudies-arrayexpress

Transcription profiling by array of Streptomyces venezuelae wild type and GlnR and GlnRII mutant strains under varying conditions of nitrogen limitation

Project description:Transcriptional responses of Streptomyces venezuelae wild-type to changes in nitrogen availibility, and comparison to glnR and glnRII deleted strains.

2011-04-20 | E-MEXP-2684 | biostudies-arrayexpress

Comparison of Aspergillus fumigatus transcriptome grown on selected nitrogen sources

Project description:Transcriptome of A. fumigatus shifted from ammoniumtartrate to different nitrogen sources and incubated for a defined time was compared. After 16h preculture, the fungus was transferred into fresh medium containing ammonium tartrate, sodium nitrate, proline or bsa as nitrogen source. After 1h, fungus was reisolated, RNA was prepared from fungus, transcriptome was assessed and used for further analysis. Ammoniumtartrate, sodiumnitrate, BSA and proline as nitrogen sources, 2 biological replicates for each source. A. fumigatus liquid media shifts were performed according to ref. (Narendja et al.,2002) with minor modifications: 200 ml minimal medium base with 5 mM ammonium tartrate was inoculated with 10^8 conidia freshly harvested. A. fumigatus ATCC 46645 conidia were grown at 37°C and 150 rpm for 16 hours. This pre-culture was then harvested, washed liberally with sterile saline and divided into mycelial masses of equal size on a sterile surface. The portions were then added to 100 ml of minimal medium base without nitrogen source. When a defined carbon source was needed, 1% glucose was added. Flasks were incubated for 20 min at 37°C. Thereafter, one of the following sterile nitrogen sources was added: ammonium tartrate to a final concentration of 5 mM, Sodiumnitrate to a final concentration of 10 mM, 1 g proline suspended in 2 ml minimal medium base, or 0.5 g BSA (Albumin Fraktion V, Roth), suspended in 15 ml minimal medium base. The cultures were incubated for another 60 minutes, harvested by filtering through Miracloth, snap frozen in liquid nitrogen, and ground using a cooled mortar to obtain a fine powder.

2011-10-29 | E-GEOD-30384 | biostudies-arrayexpress

Geobacter sulfurreducens grown in various conditions: gene expression and RpoN ChIP-chip

Project description:This SuperSeries is composed of the following subset Series: GSE17834: Transcriptome analysis of Geobacter sulfurreducens grown with different nitrogen sources GSE17837: ChIP-chip of Geobacter sulfurreducens PCA with antibody against RpoN under various conditions. Refer to individual Series

2010-06-28 | E-GEOD-17838 | biostudies-arrayexpress

RNA-seq analysis of MG1655 Escherichia coli (Wild-type and mutant lacking the RNA chaperone Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutant lacking the prominent RNA chaperone, Hfq, in bacteria that had been exposed to short-term (20min, N-) and long-term (24hr, N-24) nitrogen starvation, and following replenishment of nitrogen to long-term starved bacteria (~2hrs, N-24+2) in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of Hfq was to bacteria experiencing nitrogen starvation.

2023-12-01 | E-MTAB-13527 | biostudies-arrayexpress

Transcriptome analysis of Geobacter sulfurreducens grown with different nitrogen sources

Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire G.sulfurreducens genome with different nitrogen sources, including NH3, Gln, Asp and N2. A twelve chip study using total RNA recovered from four separate culture conditions of G.Sulfurreducens. G.Sulfurreducens PCA were harvested at mid-exponential phase. The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures)

2010-06-30 | E-GEOD-17834 | biostudies-arrayexpress

Transcriptional profiles of Haloferax mediterranei based on nitrogen availability

Project description:Transcriptional profiling of Haloferax mediterranei in three culture media with different nitrogen sources: a) cells were grown stationary and exponentially on ammonium, b) cells were grown exponentially on nitrate, and c) cells were shifted to nitrogen starvation conditions. The main differences in the transcriptional profiles have been identified between the cultures with ammonium as nitrogen source and the cultures with nitrate or nitrogen starvation, supporting previous results which indicate the absence of ammonium as the factor causing the expression of genes involved in nitrate assimilation pathway. Four-conditions experiment with four biological replicates, combined in a loop design.

2016-07-01 | E-GEOD-59551 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data