Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress exemplified by 1-butanol exposure

ABSTRACT: To study the cellular global response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius upon solvent exposure we performed transcriptome comparing the response of planktonic and biofilm cells in absence and presence 1-butanol. S. acidocaldarius was grown in Petri dishes (static incubation) in the absence and presence of 0.5% and 1% (v/v) 1-butanol at 76°C for four days. Planktonic and biofilm cells were harvested and the transcriptional response towards 1-butanol was analysed via RNA-seq. In detail:Biofilm and planktonic cell samples (supernatant after static incubation) were generated in Petri dishes (92 x 16 mm, Polystyrene, without cams, Sarstedt) as described before. Cells grown under six different conditions, including Biofilm-Control (BF0), Biofilm-0.5% (v/v) 1-Butanol (BF05), Biofilm-1% (v/v) 1-Butanol (BF1), Planktonic-Control (PL0), Planktonic-0.5% (v/v) 1-Butanol (PL05), Planktonic-1% (v/v) 1-Butanol (PL1), were seperated, harvested by centrifugation (10 min, 5,000 x g, 4 °C) and immediately frozen at -70 °C. Isolation of cells was performed in triplicates with ten technical replicas each. Samples were pooled to obtain sufficient cell mass for further processing. RNA was isolated using Trizol (Thermo Fisher Scientific). In accordance, sequencing libraries were prepared via Illumina TruSeq stranded mRNA using Ribozero for RNA depletion. Sequencing was performed on a MiSeq instrument (Illumina, San Diego, California, USA) using v3 chemistry with a read length of 2x76 nt.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Sulfolobus acidocaldarius DSM 639

SUBMITTER: Tobias Busche

PROVIDER: E-MTAB-10093 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress

Project description:In this study, we used S. acidocaldarius adapted to two extremes, low pH and high temperature, to study its tolerance and robustness as well as its global cellular response towards organic solvents exemplified by 1-butanol. We were able to identify biofilm formation as primary cellular response to 1-butanol.

2021-03-15 | PXD023858 | Pride

Escherichia coli biofilms vs planktonic culture

Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol. Two condition experiments: E. coli biofilm vs E. coli planktonic cultures. Two biological replicates with independently grown and harvested biofilms or planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.

2013-12-30 | E-GEOD-24914 | biostudies-arrayexpress

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [I]

Project description:Immobilization of Clostridium acetobutylicum B3 onto fibrous matrix by surface-adsorption was developed and applied to biobutanol production. The immobilized C. acetobutylicum B3 cells formed biofilm and showed dramatically improved butanol tolerance and production rate. DNA array-based transcriptional analysis of C.acetobutylicum B3 biofilm cells was conducted to elucidate the gene expression profile of the biofilm cells. Results showed that about 16% of the whole genome was differentially expressed. The most apparently differentially expressed genes were involved in amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, and coenzyme transport and metabolism. Samples for biofilm cells and planktonic cells were withdrawn at four diffierent fermentation phases. The gene expression pattern of biofilm cells were investigated relative to that of planktonic cells from the same phase. The experiment was carried out twice independently. Cotton fibrous matrix (60 g/L) was used as biofilm carrier.

2015-05-15 | E-GEOD-68899 | biostudies-arrayexpress

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [II]

2015-05-15 | E-GEOD-68900 | biostudies-arrayexpress

Increased mutability of staphylococci in biofilms as a consequence of oxidative stress

Project description:In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies increased mutability in the biofilm. Transcriptional profiling revealed upregulation of the superoxide dismutase gene, sodA, in early biofilm cultures, also suggesting enhanced oxidative stress in these cultures. However, loss of the genes encoding superoxide dismutases or peroxidases did not specifically exacerabate biofilm mutability. In S. aureus SH1000, hydrogen peroxide was found to contribute to biofilm mutability. Three growth conditions (18 hr planktonic growth, 48 hr biofilm growth and 144 biofilm growth) of which there are three biological replicates of each

2012-03-01 | E-GEOD-35837 | biostudies-arrayexpress

Expression changes during Candida albicans biofilm formation

Project description:The planktonic versus biofilm gene expression arrays were performed in a/alpha cell types. Gene expression arrays were performed on planktonic vs biofilm cells grown in Spider medium at 37C. Normalized data is reported in matrix. Biofilm strains (48 hour biofilms) were compared to planktonic strains (log phase planktonic cells) in Spider medium at 37C.

2011-07-08 | E-GEOD-30474 | biostudies-arrayexpress

E coli MG1655 biofilm and planktonic gene expression

Project description:Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility). Transcriptional profiling of duplicate biofilm and planktonic cultures of E. coli MG1655 grown in serine-limited MOPS minimal media.

2010-06-21 | E-GEOD-18362 | biostudies-arrayexpress

Haemophilus parasuis F9 transcriptome in biofilm and planktonic cultures using RNA sequencing

Project description:Purpose: Study transcriptome differences between biofilm, planktonic and stationary cultures. Methods: Total mRNA from in vitro cultures was extracted and sequenced using Ion Torrent PGM sequencer. Results: Characteristic transcriptomic profile was observed for biofilm, planktonic and stationary cultures. Biofilm and planktonic were similar biological states. Conclusions: Results suggest that H. parasuis F9 has more active metabolism during biofilm or planktonic growth when compared to stationary culture. Some identified membrane-related genes could play an important role in biofilm life. RNA profiles of 36 hours biofilm or planktonic cultures were generated and compared with stationary culture profile.

2014-04-02 | E-GEOD-56428 | biostudies-arrayexpress

A large-scale overexpression screen uncovers two paralogous genes ZCF15 and ZCF26 modulating Candida albicans biofilm gene circuitry (RNA-seq data)

Project description:To identify novel genes modulating Candida albicans biofilm formation, a screen of 2451 overexpression strains allowed us to identify 16 genes whose overexpression significantly reduced biofilm formation. Genome-wide expression and binding analyses were conducted upon overexpression of ZCF15 and ZCF26 and wild type planktonic and biofilm cells were performed. This study has identified new sets of biofilm regulators, including ZCF15 and ZCF26 whose specific role in metabolic remodelling during C. Albicans biofilm development. Triplicates data of RNAseq data are provided here with 6 conditions including the ZCF15 and ZCF16 cases mentioned here above

2022-06-01 | E-MTAB-11383 | biostudies-arrayexpress

Escherichia coli biofilms vs planktonic culture

2013-12-30 | GSE24914 | GEO