Halo_itraq1
Ontology highlight
ABSTRACT:
INSTRUMENT(S): ABI QSTAR
ORGANISM(S): Halobacterium Nrc-1 (halobacterium)
SUBMITTER: Amy Schmidt, Nitin Baliga
PROVIDER: PAe000253 | PeptideAtlas |
REPOSITORIES: PeptideAtlas
Similar Datasets
Project description:Macrophages are innate immune cells characterized by their plasticity and their ability to react to various environmental stimuli. These cells are involved in a multiple number of tissular functions in homeostasis and pathological contexts. According to their environment these cells could be polarized toward different states of activation which determine their functional orientation. A large part of the macrophage biology field is devoted to better define what polarizations are, from a molecular point of view. It is now accepted that a multidimensional model of polarization is needed to grasp the broad phenotype repertoire depending on various environmental signals. Oxygen tension is one of these tissular environmental parameters. We designed this study to obtain a proteomic signature of various polarizations in human monocytes derived macrophages. We also seek to explore how environmental oxygen tension varying from an atmospheric composition (18.6% O2) to a “tissular normoxia” (3% O2) could modify our classification of macrophages’ polarization. We have obtained various polarization specific proteins and oxygen sensors for human macrophages. One example is arachidonate 15-lipoxygenase (ALOX15) which is a IL4/IL13 polarization specific proteins up regulated under low oxygen exposure associated to an increase of the phagocytosis rate of apoptotic cells. These results illustrate the necessity to take into account physicochemical parameters like oxygen when macrophage polarization is studied to correctly assess their functions in tissues.
2017-09-11 | PXD006354 | Pride
Project description:We performed high-time-resolution (HTR) transcriptome analyses of Pseudomonas aeruginosa PAO1 (PA) in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT). From those genes responsive to both transient conditions, we identified 85 essential oxygen-availability responsive genes (EORGs), including the expected ones (arcDABC) encoding enzymes for arginine fermentation. We then predicted a highly accurate regulatory network for the EORGs of PA by integrating information from binding motif searching, literature and inverted HTR datasets. These results not only reveal stringent EORGs of PA and their transcription regulatory network, but also highlight that achieving a high accuracy of the inferred regulatory network might be only feasible for the apparently affected regulators under the given conditions but not for all the expressed regulators in a genome scale. Pseudomonas aeruginosa PAO1 (PA) from a continuous cultivation system during two inverted oxygen-availability transitions were used for RNA extraction and hybridization on Affymetrix P. aeruginosa Genome Array . Our aim is to identify essential oxygen-availability responsive genes and to infer an accurate oxygen-responsive regulatory network. In total, 14 samples were harvested at time points 0, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80 and 90 min after switching from aerobic to microaerobic condition. After reaching a steady state (after about another four bioreactor volume exchange) under these conditions, the culture was shifted from microaerobic back to fully aerobic condition (pO2 set point value from 0.5% to 100%). A similar set of samples were taken during the reversed transition with the same time intervals.
2013-12-10 | E-GEOD-52445 | biostudies-arrayexpress
Project description:We performed high-time-resolution (HTR) transcriptome analyses of Pseudomonas aeruginosa PAO1 (PA) in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT). From those genes responsive to both transient conditions, we identified 85 essential oxygen-availability responsive genes (EORGs), including the expected ones (arcDABC) encoding enzymes for arginine fermentation. We then predicted a highly accurate regulatory network for the EORGs of PA by integrating information from binding motif searching, literature and inverted HTR datasets. These results not only reveal stringent EORGs of PA and their transcription regulatory network, but also highlight that achieving a high accuracy of the inferred regulatory network might be only feasible for the apparently affected regulators under the given conditions but not for all the expressed regulators in a genome scale.
2013-12-10 | GSE52445 | GEO
Project description:Atmospheric oxygen tension is increasingly recognized to be hyperoxic for the maintenance of in vitro cell cultures. Oxygen has broad implications on energy metabolism, cellular growth and many regulatory functions. Primary airway epithelial cells (AECs) differentiated at air-liquid interface (ALI) are the gold standard for preclinical assessment of cystic fibrosis transmembrane conductance regulatory (CFTR) modulator efficacy in CF. The fidelity of CF AECs cultured at atmospheric oxygen tension rather than at reduced oxygen tension which more closely reflect the in vivo environment has not been studied to date. This study examined the impact of ambient (21%) and low (2%) oxygen tension on the expansion and differentiation of nasal epithelial cells (hNECs) derived from 11 participants (8 with CF and 3 non-CF). hNECs expanded under normoxic and chronic hypoxic conditions demonstrated epithelial cobblestone morphology and similar proliferation rate. hNECs differentiated at hypoxia demonstrated poorer differentiation capacity (significantly thinner epithelium and lower TEER) and a shift from ciliated to secretory epithelial phenotype. Hypoxic differentiated hNECs had significantly shorter cilia length, slower beating frequency but had improved cilia coordination. CFTR functional response is altered in hypoxic differentiated hNECs. This study highlights the need to reconsider the oxygen tension used in CF primary cell cultures so as to preserve the characteristics and functional response of the cell models as we progress towards personalised medicine in CF.
2023-03-25 | PXD038852 | Pride
Project description:Atmospheric oxygen tension is increasingly recognized to be hyperoxic for the maintenance of in vitro cell cultures. Oxygen has broad implications on energy metabolism, cellular growth and many regulatory functions. Primary airway epithelial cells (AECs) differentiated at air-liquid interface (ALI) are the gold standard for preclinical assessment of cystic fibrosis transmembrane conductance regulatory (CFTR) modulator efficacy in CF. The fidelity of CF AECs cultured at atmospheric oxygen tension rather than at reduced oxygen tension which more closely reflect the in vivo environment has not been studied to date. This study examined the impact of ambient (21%) and low (2%) oxygen tension on the expansion and differentiation of nasal epithelial cells (hNECs) derived from 11 participants (8 with CF and 3 non-CF). hNECs expanded under normoxic and chronic hypoxic conditions demonstrated epithelial cobblestone morphology and similar proliferation rate. hNECs differentiated at hypoxia demonstrated poorer differentiation capacity (significantly thinner epithelium and lower TEER) and a shift from ciliated to secretory epithelial phenotype. Hypoxic differentiated hNECs had significantly shorter cilia length, slower beating frequency but had improved cilia coordination. CFTR functional response is altered in hypoxic differentiated hNECs. This study highlights the need to reconsider the oxygen tension used in CF primary cell cultures so as to preserve the characteristics and functional response of the cell models as we progress towards personalised medicine in CF.
2023-03-25 | PXD038893 | Pride
Project description:Here we evaluated effects of the adapation of bovine embryonic stem cells (bESC) previously derived on mouse embryonic fibroblasts (MEF) under high oxygen (21%) conditions in low oxygen environment (5%) and their their molecular profile. Primed bESC established on MEF were adapted to 5% O2 conditions after 5-6 passages. Following culture in low oxygen for 5 passages, bESC were transitioned to feeder-free conditions. Comparing the transcriptomes of bESC cultured in , we found that adaptation to feeder-free conditions triggered commitment towards cell differentiation. Transition of bESC on MEF to a low oxygen environment did not result in changes in morphology or growth. Furthermore, we noted fewer changes in the transcriptome of cells grown on MEF compared to those grown in feeder-free conditions when maintained in low oxygen, compared to cells maintained in atmospheric oxygen. Lastly, while low oxygen tension did not alter the pluripotency profile of bESC, it did promote changes in transcripts related to energetic metabolism. These findings enhance our understanding about the optimal conditions for bESC culture and emphasize the importance of oxygen tension for derivation, maintenance, and performance of embryonic stem cells.
2026-06-10 | GSE310875 | GEO
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletions of phr1 and phr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7716 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phr1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 ?g of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (?) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7714 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of boa1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7723 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phoR was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7730 | biostudies-arrayexpress