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PROVIDER: PRJEB14732 | ENA |
REPOSITORIES: ENA
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Project description:Phenanthrene-degrading bacterium
| PRJNA20087 | ENA
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
Project description:Two synthetic bacterial consortia (SC) composed by bacterial strains isolated from a natural phenanthrene-degrading consortium (CON), Sphingobium sp. AM, Klebsiella aerogenes B, Pseudomonas sp. Bc-h and T, Burkholderia sp. Bk and Inquilinus limosus Inq were grown in LMM supplemented with 200 mg/L of phenanthrene (PHN) during 72 hours in triplicate.
2021-09-09 | PXD022882 | Pride
Project description:Verma2016 - Ca(2+) Signal Propagation Along Hepatocyte Cords
This model is described in the article:
Computational Modeling of
Spatiotemporal Ca(2+) Signal Propagation Along Hepatocyte
Cords.
Verma A, Makadia H, Hoek JB,
Ogunnaike BA, Vadigepalli R.
IEEE Trans Biomed Eng 2016 Oct; 63(10):
2047-2055
Abstract:
The purpose of this study is to model the dynamics of
lobular Ca(2+) wave propagation induced by an extracellular
stimulus, and to analyze the effect of spatially systematic
variations in cell-intrinsic signaling parameters on sinusoidal
Ca(2+) response.We developed a computational model of lobular
scale Ca(2+) signaling that accounts for receptor- mediated
initiation of cell-intrinsic Ca(2+) signal in hepatocytes and
its propagation to neighboring hepatocytes through gap
junction-mediated molecular exchange.Analysis of the
simulations showed that a pericentral-to-periportal spatial
gradient in hormone sensitivity and/or rates of IP3 synthesis
underlies the Ca(2+) wave propagation. We simulated specific
cases corresponding to localized disruptions in the graded
pattern of these parameters along a hepatic sinusoid.
Simulations incorporating locally altered parameters exhibited
Ca(2+) waves that do not propagate throughout the hepatic
plate. Increased gap junction coupling restored normal Ca(2+)
wave propagation when hepatocytes with low Ca(2+) signaling
ability were localized in the midlobular or the pericentral
region.Multiple spatial patterns in intracellular signaling
parameters can lead to Ca(2+) wave propagation that is
consistent with the experimentally observed spatial patterns of
Ca(2+) dynamics. Based on simulations and analysis, we predict
that increased gap junction-mediated intercellular coupling can
induce robust Ca(2+) signals in otherwise poorly responsive
hepatocytes, at least partly restoring the sinusoidally
oriented Ca (2+) waves.Our bottom-up model of agonist-evoked
spatial Ca(2+) patterns can be integrated with detailed
descriptions of liver histology to study Ca(2+) regulation at
the tissue level.
This model is hosted on
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MODEL1603110003.
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2024-09-02 | BIOMD0000000834 | BioModels
Project description:Inter-chromosomal contacts demarcate genome topology along a spatial gradient
| PRJNA1013014 | ENA
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
Project description:Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity.We investigate thermal acclimation of three species of Takydromus lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism,organ, mitochondria, metabolome, and proteome.
2021-12-12 | PXD029083 | Pride