Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of Bacillus subtilis in response to physical plasma treatment

ABSTRACT: In this study, we introduce for the first time a growth chamber system suitable for physical plasma treatment of bacteria in liquid medium. Bacillus subtilis 168 cells were treated with argon plasma in order to investigate their specific stress response usong a proteomic and transcriptomic approach. The treatment with three different discharge voltages revealed not only growth differences, but also clear cellular stress responses. B. subtilis faces severe cell wall stress, which was made visible alsoelectron microscopy, DNA damages and oxidative stress. The biological findings could be supported by the reactive plasma species, found by plasma diagnostics, i.e. optical emission spectroscopy (OES) and Fourier transformed infrared spectroscopy (FTIR).

ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168 Bacillus subtilis

PROVIDER: GSE27113 | GEO | 2011/06/01

SECONDARY ACCESSION(S): PRJNA137433

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome analysis of Bacillus subtilis in response to physical plasma treatment

Project description:In this study, we introduce for the first time a growth chamber system suitable for physical plasma treatment of bacteria in liquid medium. Bacillus subtilis 168 cells were treated with argon plasma in order to investigate their specific stress response usong a proteomic and transcriptomic approach. The treatment with three different discharge voltages revealed not only growth differences, but also clear cellular stress responses. B. subtilis faces severe cell wall stress, which was made visible alsoelectron microscopy, DNA damages and oxidative stress. The biological findings could be supported by the reactive plasma species, found by plasma diagnostics, i.e. optical emission spectroscopy (OES) and Fourier transformed infrared spectroscopy (FTIR). Cells were grown in LB medium. At OD540 of 0.5, argon plasma treatment was set for 15 min with a discharge power of 5 W. Samples for mircroarray analysis were taken 5 min after the 15 min plasma treatment. Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all samples was labeled with Cy3.

2011-06-01 | E-GEOD-27113 | biostudies-arrayexpress

Transcriptome analysis of Bacillus subtilis in response to air plasma treatment

Project description:In this study, we present a follow up investigation on the effects of argon plasma on vegetative growing Bacillus subtilis 168 (see GSE27113). A growth chamber system suitable for low temperature gas plasma treatment of bacteria in liquid medium enabled a first glimpse on the complex cellular response. In order to gain further knowledge, a second kind of plasma treatment was applied and combined proteomic and transcriptomic analyses were used to investigate the specific stress response of B. subtilis cells to treatment with not only argon but also air plasma. Besides similar cellular responses, due to both argon and air plasma treatment, a variety of different responses such as growth retardation and morphological changes were observed. Furthermore, we analyzed the specific response to DNA damages and oxidative stress. The biological findings such as oxidative stress responses were supported by the detection of reactive plasma species by OES and FTIR measurements. Cells were grown in LB medium. At OD540 of 0.5, air plasma treatment was set for 15 min with a discharge power of 7.4 W. Samples for mircroarray analysis were taken 5 min after the 15 min plasma treatment. Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all samples was labeled with Cy3.

2013-08-22 | E-GEOD-32865 | biostudies-arrayexpress

Transcriptome analysis of Bacillus subtilis in response to air plasma treatment

2013-08-22 | GSE32865 | GEO

Project description:Contribution of Fourier transform infrared spectroscopy for outbreak investigation of carbapenem-resistant Acinetobacter baumannii

| PRJNA1172467 | ENA

Project description:Clostridioides difficile investigation by FTIR spectroscopy

| PRJNA1199010 | ENA

Probing Blood Plasma Protein Glycosylation with Infrared Spectroscopy

Project description:The health state of an individual is closely linked to the glycosylation patterns of their blood plasma proteins. However, obtaining this information requires cost- and time-efficient analytical methods. We put forward infrared spectroscopy, which allows label-free analysis of protein glycosylation, but so far has only been applied to analyses of individual proteins. Although spectral information does not directly provide the molecular structure of the glycans, it is sensitive to changes therein and covers all types of glycosidic linkages. Combining single-step ion exchange chromatography with infrared spectroscopy, we developed a workflow that enables separation and analysis of major protein classes in blood plasma. Our results demonstrate that infrared spectroscopy can identify different patterns and global levels of glycosylation of intact plasma proteins. To showcase the strengths and limitations of the proposed approach, we compare the glycoforms of human and bovine alpha-1-acid glycoproteins, which exhibit highly variable global levels of glycosylation. To further independently evaluate our conclusions, the glycan moieties of human alpha-1-acid glycoprotein were further analyzed using established glycomics workflow. Importantly, the chromatographic separation of blood plasma improves the detection of aberrant glycoforms of a given protein, as compared to infrared spectroscopy of bulk plasma. The presented approach allows time-efficient comparison of glycosylation patterns of multiple plasma proteins, opening new avenues for biomedical probing.

2024-02-26 | PXD046796 | Pride

Project description:Evaluation of Fourier-Transform Infrared Spectroscopy (FT-IR) as a Control Measure for Nosocomial Outbreak Investigations

| PRJNA989739 | ENA

Plasma functionalization of PCL nanofibers changes protein interactions with cells resulting in increased cell viability

Project description:The surface properties of electrospun scaffolds can greatly influence protein adsorption and thus strongly dictate cell-material interactions. In this study, we aim to investigate possible correlations between the surface properties of argon, nitrogen and ammonia/helium plasma-functionalized polycaprolactone (PCL) nanofibers and their cellular interactions by examining the protein corona patterns of the plasma-treated nanofibers as well as the cell membrane proteins involved in cell proliferation. As a result of the performed plasma treatments, PCL nanofiber morphology was preserved while wettability was improved profoundly after all treatments because of the incorporation of polar surface groups. Depending on the discharge gas, different types of groups are incorporated which influenced the resultant cell-material interactions. Argon plasma-functionalized PCL nanofibers, only enriched by oxygen-containing functional groups, were found to show the best cell-material interactions, followed by N2 and He/NH3 plasma-treated samples. SDS-PAGE and LC-MS clearly indicated an increased protein retention compared to non-treated PCL NFs. The most differential proteins surface a distinct molecular machinery mediating the increased proliferation and viability on plasma treated NF. Finally, differential protein analysis between the different plasma’s gives a first hint into the molecular underpinning of the superior performance of Argon NF.

2018-08-29 | PXD010910 | Pride

Project description:Use of Fourier-transform infrared spectroscopy for real-time outbreak investigation of OXA-48-producing Escherichia coli

| PRJNA1028854 | ENA

Comparison of fast Fourier-Transform Infrared Spectroscopy biotyping with Whole Genome Sequencing based genotyping in common nosocomial pathogens

Project description:Comparison of fast Fourier-Transform Infrared Spectroscopy biotyping with Whole Genome Sequencing based genotyping in common nosocomial pathogens

| PRJEB51462 | ENA

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