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PROVIDER: PRJNA1013690 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide transcriptional profiling shows that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression. However, simulation experiments on ground, without space constraints, show weaker effects than space environment. A global and integrative analysis using the M-bM-^@M-^\gene expression dynamics inspectorM-bM-^@M-^] (GEDI) self-organizing maps, reveals a subtle response of the transcriptome using different populations and microgravity and hypergravity simulation devices. These results suggest that, in addition to behavioural responses that can be detected also at the gene expression level, the transcriptome is finely tuned to normal gravity. The alteration of this constant parameter on Earth can have effects on gene expression that depends both on the environmental conditions and the ground based facility used to compensate the gravity vector. Alternative and commons effects of mechanical facilities, like the Random Positioning Machine and a centrifuge, and strong magnetic field ones, like a cryogenically cooled superconductive magnet, are discussed. We compare the effects over the gene expression profile of different gender/age Drosophila imagoes in 3-4 days-long experiments under altered gravity conditions into three GBF ("Ground Based Facilities" for micro/hyper- gravity simulation) using whole genome microarray platforms. Descriptions of different GBFs ("treatments"): LDC means "Large Diameter Centrifuge". Samples can be placed under three conditions: inside LDC (at certain g level), at the LDC rotational control and at external 1g control (outside the LDC). RPM means "Random Positioning Machine". Samples can be placed under two conditions: inside RPM (at nearly 0g, Microgravity level) and at external 1g control (outside the RPM). At the magnet, means INSIDE the Magnetic levitator (another GBF). Samples can be placed under four conditions: inside Magnet 0g* (at microgravity with magnetic field), inside Magnet at 1g* (internal control with magnetic field) or inside the magnet 2g* (at hypergravity with magnetic field) and at external 1g control (outside the magnet)
2013-06-26 | E-GEOD-33801 | biostudies-arrayexpress
Project description:C. albicans is a dimorphic yeast which can switch from budding yeast and to hyphal forms and this property is essential for biofilm establishment and maturation. C. albicans undergoes this yeast-to-hyphal switch in response to high CO2. The purpose of this study is to use RNA-seq to investigate pathways whose genes are differentially expressed when C. albicans biofilms are grown in a physiologically relevant elevated (5%) CO2 environment compared to a low/atmospheric (0.03%) CO2 environment. We report that in C.albicans biofilms grown under 5% CO2 conditions, genes controlled by core biofilm regulatory transcription factors such as Brg1, Efg1, Ndt80, and Bcr1 are overall expressed at significantly higher levels compared to those grown in 0.03% CO2 conditions. We find that genes encoding glucose and amino acid transporters, as well as genes previously found to be involved in the response to Ketoconazole treatment, are significantly upregulated in 5% CO2 C. albicans biofilms. Overall, these data suggest a high CO2 environment enhances biofilm formation of C. albicans and may also increase antifungal tolerance of such biofilms.
2021-04-14 | GSE172004 | GEO
Project description:Atmospheric CO2 concentrations can determine the number of stomata that form on plant leaves (Woodward & Kelly 1995 New Phyt 131: 311-327). The majority of species exhibit reduced stomatal densities at elevated CO2. However, not all plant species react in the same way to elevated CO2 levels and there is a spectrum of effects: Some species increase stomatal densities, some decrease stomatal densities, and some are unaffected. In addition to which, other environmental factors influence the number of stomata that a plant form. Light intensity has also been shown to affect stomatal numbers in various Arabidopsis ecotypes (Schluter et al. 2003 J Exp Bot 54 (383): 867-874; Lake et al. 2002 J Exp Bot 53 (367): 183-193), by increasing stomatal numbers with increasing light levels. There are many changes in gene expression under elevated CO2 conditions, so pinpointing specific genes involved in the stomatal response to CO2 is difficult. In addition, if there is crosstalk between the various signalling pathways affecting ultimate stomatal numbers this complicates further the task of finding genes specifically involved the stomatal response to CO2. Therefore we propose to look at the interaction of two known influences on stomatal numbers, light and CO2, on one specific ecotype, Col-0. We aim to test the hypothesis that light signals interact the CO2 signals that affect stomatal development. Arabidopsis thaliana Columbia-0 ecotype has previously been shown to decrease stomatal numbers in response to a doubling of ambient CO2 concentrations. Col-0 has also been shown to increase stomatal numbers in response to high light intensities. Therefore we propose to grow A. thaliana Col-0 at three light intensities (50 mmol m-2 s-1, 150 mmol m-2 s-1 and 250 mmol m-2 s-1), in both ambient and elevated (double ambient) atmospheric CO2 concentrations. By looking in more detail at how gene expression differs between plants grown at ambient and elevated CO2 at the same light intensities, and also how gene expression differs between plants grown at the same CO2 concentration but different light intensities, we aim to identify those genes involved in the stomatal developmental response to CO2 and whether genes involved in the light response can also be isolated. Experimenter name = Susannah Bird Experimenter phone = (0114) 222 4649 Experimenter address = Animal and Plant Science Department Experimenter address = Alfred Denny Building Experimenter address = Western Bank Experimenter address = Sheffield Experimenter zip/postal_code = S10 2TN Experimenter country = UK Keywords: growth_condition_design
2007-01-08 | GSE5733 | GEO
Project description:We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance.
2012-08-10 | GSE33927 | GEO
Project description:To investigate the transcriptome changes by CO2 supply, we evaluated the transcriptional changes in fennel. We then performed gene expression profiling analysis using data obtained from RNA-seq of fennel at two stress conditions.
2022-11-23 | GSE218441 | GEO
Project description:Purpose: The goal of this study was to use RNA-seq to define the Klebsiella pneumoniae transcriptome recorded under 5 different experimental conditions, and to identify signature genes of each condition by comparing global transcriptional profiles. Methods: mRNA profiles were generated for Klebsiella pneumoniae CH1034 clinical isolate, in triplicate, by deep sequencing. Total RNAs were harvested from bacteria cultured at 37°C in M63B1 minimal media under different conditions: (i) planktonic aerobic condition at OD 620nm=0.250 (exponential growth-phase), (ii) overnight planktonic aerobic condition (stationnary growth-phase), (iii) biofilm in a flow-cell chamber after 7 hours of incubation (7-hours old biofilm), (iv) biofilm in a flow-cell chamber after 13 hours of incubation (13-hours old biofilm), (v) bacteria self-dispersed from biofilm recovered in the flow-cell effluent (biofilm-dispersed bacteria). Ribosomal RNAs were removed using the Bacteria Ribo-Zero Magnetic kit (Epicentre Biotechnologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), and 50bp single-reads were obtained by HiSeq 2000 (Illumina).The sequence reads that passed FastQC quality filters were mapped to the CH1034 genome using BurrowsâWheeler Aligner (BWA) (0.7.12-r1039 version). The transcript levels were determined using HTSeq-count (0.6.1p1 version) with union mode followed by DESeq (1.16.0 version) analysis. qRTâPCR validation was performed using SYBR Green assays. Results: We found that each condition has a specific transcriptional profile, and we identify 4 robust signature genes for each. Conclusion: Our study represents the first detailed analysis of K. pneumoniae transcriptomes under different experimental conditions generated by RNA-seq technology. The data reported here should permit the dissection of complex biologic functions involved in the transition between the sessile and planktonic modes of growth. Determination of the transcriptional profiling of Klebsiella pneumoniae under 5 different experimental conditions. mRNA profiles were generated for bacteria under exponential planktonic growth-phase, stationary planktonic growth-phase, 7 hours-old biofilm, 13 hours-old biofilm and biofilm-dispersed modes, each in three biological replicates, by deep sequencing using Illumina HiSeq
2016-03-03 | E-GEOD-71754 | biostudies-arrayexpress
Project description:Diatoms are a major primary producer accounting for 20% of the global primary production. Their massive carbon fixation is driven by the CO2-concentrating mechanisms (CCM), in which CO2 is actively supplied to the Rubisco localized in the pyrenoid, a membrane-less organelle of the plastid. To promote CO2 fixation, CO2 concentration in the pyrenoid matrix is assumed to be elevated while leakage of CO2 is minimized. However, due to the lack of information on the structural basis of diatom pyrenoid, the mechanism allowing efficient CO2 supply in conjunction with pyrenoid structure remains to be elucidated. While isolation of diatom pyrenoid is technically difficult due to structural instability, here we applied in vivo crosslinking using photo amino acids (pAA) which enabled us to obtain Rubisco enriched fractions. Based on LC-MS/MS analysis of the RbcL-enriched fraction, we identified a novel protein that surrounds the pyrenoid like a shell and hence named a Pyshell (Pyrenoid shell). Using genome-edited mutants, Pyshell was demonstrated to be a critical component required for growth under CO2-limiting conditions. The comprehensive analysis and identification of the pyrenoid component gave an important insight into the molecular basis driving the oceanic primary production.
2024-05-04 | PXD041920 | JPOST Repository
Project description:We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance. Both 137c wild type (cc125) and cia5 mutant were induced for 4 hours induction under H-CO2 (5%), L-CO2 (300~500 ppm), and VL-CO2 (100~200 ppm) conditions. 2 biological replicates were done for each strain -CO2 combination.
2012-08-10 | E-GEOD-33927 | biostudies-arrayexpress