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Transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon short-term starvation stress

ABSTRACT: This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to short-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 4h after growth on a rich medium. Survival was monitored by plating and transcriptomic response was determined by whole-genome microarray analysis. The data showed no major differences were obsrved in gene expression and the viability of the cells were not affected during short-term incubation time

ORGANISM(S): Sphingomonas sp. LH128

PROVIDER: GSE44310 | GEO | 2013/02/14

SECONDARY ACCESSION(S): PRJNA189419

REPOSITORIES: GEO

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Transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon short-term starvation stress

Project description:This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to short-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 4h after growth on a rich medium. Survival was monitored by plating and transcriptomic response was determined by whole-genome microarray analysis. The data showed no major differences were obsrved in gene expression and the viability of the cells were not affected during short-term incubation time Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 starved for 4h in isotonic solution of 0.01 mM MgS04 was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium to an OD600 of 0.5, washed twice with 0.01 mM MgS04 and resuspended in the same solution to an OD of 0.5. RNA was extracted both from starved cells and from the initial culture (non-starved cells) and cDNA was synthesized and labeled with Cy3. Transcriptomic response of three replicates were analyzed and compared with the initial inoculum

2013-02-14 | E-GEOD-44310 | biostudies-arrayexpress

Transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon long-term starvation stress

2012-10-25 | GSE41814 | GEO

transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon long-term starvation stress

Project description:This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to long-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 6 months after growth on a rich medium. Survival was monitored by plating, physiological response was examined by flow cytometry and FAME analysis, and this response was related to transcriptomic response as determined by whole-genome microarray analysis. The data showed that decreased gene functions involved in ribosomal proteins biosynthesis, decreased chromosomal replication, increased gene functions involved in stringent regulation of gene expression, increased gene functions involved in genetic exchange and recombination, increased efflux systems, increased degradation of rRNA, and increased M-NM-2-oxidation of fatty acids to access stored nutrients. Genes involved in PAH degradations appears to be with decreased expression. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 starved for 6 month in isotonic solution of 0.01 mM MgS04 was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium to an OD600 of 0.5, washed twice with 0.01 mM MgS04 and resuspended in the same solution to an OD of 0.5. RNA was extracted both from starved cells and from the initial culture (non-starved cells) and cDNA was synthesized and labeled with Cy3. Transcriptomic response of three replicates were analyzed and compared with the initial inoculum

2012-10-25 | E-GEOD-41814 | biostudies-arrayexpress

Biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on phenanthrene

Project description:This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 biofilms as a response to short-term and long-term solute (NaCl) stress was studied using genome-wide gene expression analysis. For this purpose, the strain was grown in customized continuous glass flow chambers that contain solid phenanthrene as a sole carbon source and that allow easy recovery of biofilm cells for transcriptomic and physiological analysis. A NaCl stress of 450 mM was imposed on LH128 biofilms growing on phenanthrene crystals coated on glass slides either for 4 hours (acute stress) or for 3 days (chronic stress). RNA was extracted from the biofilm and cDNA was synthesized and labeled with Cy3. Transcriptomic response in the stressed biofilms of three replicates per conditions were analyzed and compared with non-stressed

2012-06-18 | E-GEOD-38296 | biostudies-arrayexpress

Biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on phenanthrene

2012-06-18 | GSE38296 | GEO

Transcriptomic study of Sphingomonas sp. LH128 inoculated into phenanthrene-contaminated soil

Project description:The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. Genes with increased expression comprised of gene encoding PAH catabolic enzymes, stress resistance, oxidative stress tolerance, outer membrane proteins/porins and efflux pump proteins while the downregulated genes comprised of genes encoding flagellar biosynthesis, ribosomal proteins and ATPase. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 inoculated into phenanthrene contaminated soil after 4h and after 10 days of incubation was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium and inoculated at appropriated celld densitites. RNA was extracted both from soil and and from initial inoculum and cDNA was synthesized and labeled with Cy3. Transcriptomic response in soil of three replicates per conditions after both incubation duration were analyzed and compared with the initial inoculum

2012-10-20 | E-GEOD-41705 | biostudies-arrayexpress

Transcriptomic study of Sphingomonas sp. LH128 inoculated into phenanthrene-contaminated soil

2012-10-20 | GSE41705 | GEO

Effects of polycyclic aromatic hydrocarbons on osteoclasts and osteoblasts in the scales of zebrafish

Project description:It has been reported that polycyclic aromatic hydrocarbons (PAHs) act on calcified tissue and suppress osteoblastic activity in the scales of teleost fish. In the present study, the differentially-expressed genes in the zebrafish scales treated with benzo[c]phenanthrene (BcP), a kind of PAH, or its metabolite 3-hydroxybenzo[c]phenanthrene (3-OHBcP) were investigated using GeneChip® oligonucleotide microarrays.

2020-11-12 | GSE161253 | GEO

Sphingomonas sp. LH128

Project description:Transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon short-term starvation stress

| PRJNA189419 | ENA

HepG2 treated with Polycyclic Aromatic Hydrocarbons (PAHs)

Project description:Assessing the potential carcinogenicity of human toxins represents an ongoing challenge. Chronic rodent bioassays predict human cancer risk with limited reliability, and are expensive and time-consuming. To identify alternative prediction methods, we evaluated a transcriptomics-based human in vitro model to classify carcinogens by their modes of action. The aim of this study was to determine the transcriptomic response and identify specific molecular signatures of polycyclic aromatic hydrocarbons (PAHs), which can be used as predictors of carcinogenicity of environmental toxins in human in vitro systems. We found that characteristic molecular signatures facilitate identification and prediction of carcinogens. To evaluate the change in gene expression levels, human hepatocellular carcinoma (HepG2) cells were exposed to nine different PAHs (benzo[a]pyrene, dibenzo[a,h]anthracene, 3-methylcholanthrene, naphthalene, chrysene, phenanthrene, benzo[a]anthracene, benzo[k]fluoranthene, and indeno[1,2,3-c,d]pyrene) for 48 h. Gene expression analysis was conducted using a 44K whole human genome microarray (Agilent Technologies, USA).

2012-04-17 | E-GEOD-37326 | biostudies-arrayexpress

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