Gene expression in Plasmodium falciparum NF54 and P. falciparum HOX
ABSTRACT: P. falciparum NF54 proliferates under micro-aerophilic conditions in an environment of 3% O2, 4% CO2, 93% N2. This strain was gradually adapted to proliferate under standard tissue culture conditions of 5% CO2/95% air (~19% O2) to generate P. falciparum HOX. We compared global gene expression profiles of the two strains to identify differences, if any. Asynchronous cultures of P. falciparum NF54 and HOX propagated in O+ RBCs were processed and gene expression analyzed on Affymetrix microarrays. All cultures consised of 80% rings + trophozoites.
Project description:Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation ≈ 260 µmol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (≈ 13 µmol l-1). Dynamics of low and high O2 responses of A. fumigatus cultivated in an O2-controlled fermenter
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy. Two biological replicates of timecourses under four conditions: medium bubbled with air (control) or three experimental gases (low CO2; low O2; or low CO2 and low O2)
Project description:Transcriptional profiling of P. falciparum comparing parasites exposed to 5% and 21% oxygen environmental conditions in the late ring stage. Two experimental conditions: 5% vs 21%. Biological replicates: 3 normoxia and 3 hyperoxia replicates
Project description:Ischemia exists in many diseased tissues including arthritic joints, atherosclerotic plaques and malignant tumors. Macrophages accumulate in these sites and upregulate genes in response to the hypoxia present. We used microarrays to detail the hypoxia upregulated gene in human primary macrophages. Experiment Overall Design: Primary macrophages were differentiated for 7 days in vitro from human peripheral blood (monocyte-derived macrophages, MDMs) and were subjected to severe hypoxia (< 0.5% O2) or normoxia (20.9% O2) in 5% CO2 humidified multi-gas incubators.
Project description:To delineate the role of hypoxia in esophageal epithelial biology, we carried out gene array experiments using a non-transformed immortalized diploid human esophageal cell line, EPC2-hTERT (Mol Cancer Res. 2003;1:729-38). Unlike cancer cell lines, EPC2-hTERT has no genetic alterations at early passages that may affect the cellular response to hypoxia. Experiment Overall Design: EPC2-hTERT cells were exposed to moderate (1% O2) hypoxia in experiment 1 (Exp1) or severe (0.2% O2) hypoxia in experiment 2 (Exp2). Normoxia (21% O2) served as a control in both experiments.
Project description:In this study we analyzed the effect of overexpression of an HA-tagged version of the ERF RAP2.12 on the transcriptome levels in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes. We also analyzed the effect of a RAP2.12 and RAP2.2 simultaneous silencing in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes. We treated Arabidopsis Col-0 (wt) rosettes and transgenic HA::RAP2.12 and amiRAP2.2-12 , 5-week old, grown in 8/16 light/dark photoperiod with: -Control (22°C, dark, 21% O2, 1.5h). -Hypoxia (22°C, dark, 1% O2, 1.5h).
Project description:We compared transcript levels at several points along the asexual blood cycle between 21 P. falciparum lines. These 21 parasite lines are organized in 4 sets of parasite lines, with all parasite lines within a set sharing a clonal origin. We compared transcript levels within each set. We also performed comparative genome hybridization (CGH) for all 21 parasite lines.
Project description:Sorafenib leads to a survival benefit in patients with advanced hepatocellular carcinoma but its use is hampered by the occurrence of drug resistance. To investigate the molecular mechanisms involved we developed five resistant human liver cell lines in which we studied morphology, gene expression and invasive potential. The cells changed their appearance, lost E-cadherin and KRT19 and showed high expression of vimentin, indicating epithelial-to-mesenchymal transition. Resistant cells showed reduced adherent growth, became more invasive and lost liver-specific gene expression. Furthermore, following withdrawal of sorafenib, the resistant cells showed rebound growth, a phenomenon also found in patients. This cell model was further used to investigate strategies for restoration of sensitivity to sorafenib. We determined gene expression profiles for 13 samples, grown in 1x106 in 25 cm² tissue flasks. Three flasks contained control samples: HepG2 cells at 20% O2/ 5% CO2/ 75% N2, not exposed to sorafenib. Four flasks contained samples from condition 1: HepG2S1 cells at 20% O2/ 5% CO2/ 75% N2, exposed to sorafenib. Three flasks contained samples from condition 2: HepG2S1 cells at 20% O2/ 5% CO2/ 75% N2, withdrawn from sorafenib. Three flasks contained samples from condition 3: HepG2S1 cells at 2% O2/ 5% CO2/ 93% N2, exposed to sorafenib.