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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Light versus Dark gene expression in SAR11

ABSTRACT: We investigated the transcriptional response of cand. Pelagibacter ubique cultures to light and dark when grown under carbon replete and deplete conditions. Results: During exponential phase, few genes were differentially transcribed between light:dark growth conditions. In stationary phase, a high proportion (9.7%) of coding sequences were found differentially expressed between treatments; 4.7% being up-regulated in the light (n=64) and 4.9% being up-regulated in the dark (n=67). Several components of the oxidative phosphorylation pathway were up-regulated in the dark, supporting physiological data showing higher respiration rates in darkness than in the light under starvation conditions. We also observed up-regulation of a proton translocating pyrophosphate synthase (SAR11_1040), which may be an additional energy production mechanism utilized by SAR11 cells in the dark. Finally, we noted the up-regulation of pili formation genes in the array data, consistent with the observation of pili in dark grown cells via electron microscopy. Triplicate biological replicates were collected from five growth conditions (n=15 total): 1) exponential phase, 24 hour light (n=3) 2) exponential phase, 24 hour dark (n=3) 3) stationary phase, 12:12 hour light:dark cycles (n=3) 4) stationary phase, 24 hour dark (n=3) 5) stationary phase, 6 hours after transfer to darkness (n=3)

ORGANISM(S): Candidatus Pelagibacter ubique HTCC1062

SUBMITTER: Mike Schwalbach

PROVIDER: E-GEOD-24134 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Light versus Dark gene expression in SAR11

Project description:We investigated the transcriptional response of cand. Pelagibacter ubique cultures to light and dark when grown under carbon replete and deplete conditions. Results: During exponential phase, few genes were differentially transcribed between light:dark growth conditions. In stationary phase, a high proportion (9.7%) of coding sequences were found differentially expressed between treatments; 4.7% being up-regulated in the light (n=64) and 4.9% being up-regulated in the dark (n=67). Several components of the oxidative phosphorylation pathway were up-regulated in the dark, supporting physiological data showing higher respiration rates in darkness than in the light under starvation conditions. We also observed up-regulation of a proton translocating pyrophosphate synthase (SAR11_1040), which may be an additional energy production mechanism utilized by SAR11 cells in the dark. Finally, we noted the up-regulation of pili formation genes in the array data, consistent with the observation of pili in dark grown cells via electron microscopy.

2011-12-31 | GSE24134 | GEO

Diel growth of Thalassiosira pseudonana

2013-04-18 | GSE45252 | GEO

Gene expression of Vibrio parahaemolyticus in the early stationary phase

Project description:Naturally bacteria are commonly forced to remain in stationary phase. There is no increase in cell mass, however, cell division keep on. Vibrio (V.) parahaemolyticus is an aquatic bacterium capable of causing foodborne gastroenteritis outbreaks all over the world. So far, little is known about whole genomic expression of V. parahaemolyticus in the early stationary phase compared with the phase of exponential growth. Since under starvation cell sizes decrease and endogenous metabolism reduces, genes are considered to be highly repressed in the stationary phase. However, our data shows in total 172 induced genes, while 61 genes were repressed in the early stationary phase compared with exponential phase. In fatty acid and phospholipid metabolism functional category only induced genes were found, whereas in three other metabolic functional groups appeared no significant up-regulated genes (adjusted P-value<0.05). Genes in two metabolic functional categories remained stable in the early stationary phase. DAVID analyses were carried out exploring the gene regulation. In total, ten functional categories showed a total up-regulation in early stationary phase, while only three metabolic functional categories showed a down-regulation and four categories showed stably in early stationary phase. Early stationary phase gene expression was detected in total bacterial RNA of V. parahaemolyticus. Two phases (exponential phase and early stationary phase) were used in 8 biological replicates. Gene expression in exponential phase was used for normalization.

2015-01-31 | E-GEOD-65448 | biostudies-arrayexpress

mRNA Expression Data from Murine Hearts of Shiftwork MI, Normal MI and Sham Wildtype Mice at 24-hours Post-MI

Project description:Male C57Bl/6 mice were randomized to undergo 5 days of i) a shiftwork protocol (10-hour light: 10-hour dark cycle) before myocardial infarction (MI) surgery, ii) a normal 12-hour light: 12-hour dark environment before MI surgery, iii) a normal 12-hour light: 12-hour dark environment and used as sham controls, or iv) a shiftwork protocol (10-hour light: 10-hour dark cycle) and used as sham controls. MI surgery was performed on the 5th day, after which all mice were returned to a normal 12-hour light: 12-hour dark cycle. Hearts were collected 24-hours post-MI at ZT06. The microarray approach allows the investigation of transcriptome-wide gene expression changes in hearts from mice on a shiftwork cycle or on a regular light:dark cycle before MI.

2018-11-30 | GSE123092 | GEO

Gene expression of Vibrio parahaemolyticus in the early stationary phase

2015-01-31 | GSE65448 | GEO

Diel growth of Thalassiosira pseudonana

Project description:Transcript levels of all T. pseudonana genes was measured every twelve hours throughout the batch (non-chemostatic) growth of axenic cells grown in large glass bioreactors on a 12hr:12hr dark:light cycle for five days. The data were analyzed to reveal the physiological and regulatory changes that recurred in this diatom when transitioning between dark and light conditions, as well as from exponential phase to stationary, nutrient limited conditions. The longitudinal experiment was performed with two replicates, at 400 and 800ppm CO2. Two growth experiments were conducted, with 10 and 9 longitudinal samples collected from each experiment, respectively. Two-color arrays were used with dye flips for labeling. A common internal reference sample was used for one channel on each array. Expression changes for longitudinal analysis were calculated as the difference from the mean log2 expression ratio for each to the common reference sample, for each gene, over all samples within an experiment. For the analysis of diel states in T. pseudonana, samples from the two series were matched according to the time from innoculation, and divided into four classes: dawn samples (taken at the end of each dark phase), dusk samples (taken at the end of each light phase), exponential samples (the first five samples in each series prior to a drop in growth rate on Day 3), and stationary samples (all samples including following the drop in growth rate on Day 3).

2013-04-18 | E-GEOD-45252 | biostudies-arrayexpress

Streptococcus pyogenes

Project description:GAS M3 serotype, exponential versus stationary phase

| PRJNA96597 | ENA

Characterization of cell density-regulated gene expression of the grass endophyte Azoarcus sp. BH72

Project description:Azoarcus sp. BH72 is able to communicate via cell density-dependent gene regulation. Here, the impact of cell-free conditioned culture supernatants, obtained from stationary phase Azoarcus wild type cultures, on gene expression was investigated determining changes in transcript profiles when early exponential aerobic cultures were incubated with cell-free culture supernatants for one and four hours. Bacterial communication via quorum sensing (QS) is involved in the regulation of several cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. The nitrogen-fixing model endophyte of grasses Azoarcus sp. strain BH72 shows density-dependent gene regulation in the absence of common hydrophobic autoinducers for pilA encoding the structural protein of type IV pili that are essential for plant colonization. Here, we used a transcriptomic approach to identify target genes differentially regulated under QS conditions in conditioned supernatants in comparison to standard growth conditions. Analysis used RNA from the early exponential growth phase as control samples for comparison to the quorum-sensing condition samples taken at one hour and four hours after incubation with cell-free culture supernatants.

2011-12-01 | E-GEOD-25939 | biostudies-arrayexpress

Gene regulation of carbon fixation, storage and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles

Project description:Regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at cell, metabolite and gene expression level in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time-points provide a comprehensive data set on carbon incorporation, fate and regulation. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light responding genes in e.g. fatty acid biosynthesis were identified. Transcripts and cell chemistry data reflect the link between light energy availability and light energy consuming metabolic processes. Our data confirm spatial localization of processes in carbon metabolism to e.g. either plastids or mitochondria, or glycolysis/gluconeogenesis which are localized to the cytosol, chloroplast and to mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes, and mining of genes involved in light responses and circadian rhythms. Gene regulation in Phaeodactylum tricornutum was examined in cultures acclimatized to growth cycles of 16/8 hour photoperiods (16 hour light, 8 hour dark). Two biological replicas were harvested at each of the eight time points, spaning a 27 hour period. 5 of the time points (0.5 h, 3 h, 6 h, 10.5 h and 15.5 h) were harvested in the light phase, while 3 time points were harvested during the dark phase (0.5 h, 4 h and 7.5 h darkness).

2013-03-01 | E-GEOD-42514 | biostudies-arrayexpress

Rapid Response and Slow Recovery of the H3K4me3 Epigenomic Marker in the Liver After a Light-Mediated Phase Advance of the Circadian Clock

Project description:Mammalian tissues display circadian rhythms in which transcription levels rise and fall throughout a 24-hour day. These rhythms include histone modifications. Here we asked whether an advance of the light-dark cycle could alter rhythms in the liver epigenome at the H3K4me3 (trimethylation of lysine 4 on histone 3) modification, which is found at active and poised gene promoters. H3K4me3 levels were first measured at 4-time points (Zeitgeber Time [ZT] 3, 8, 15, and 20) during a normal 12L:12D light:dark cycle. Peak levels were observed during the early dark phase at ZT15, and dropped to low levels around lights-on (ZT0) between ZT20 and ZT3. A six-hour phase advance at ZT18 (new lights-on after only 6 h of darkness) led to a transient extension of peak H3K4me3 levels. Although locomotor activity re-entrained within a week after the phase advance, H3K4me3 rhythms failed to do so with peak levels remaining in the light phase at the one-week recovery time point. Eight weekly phase advances, with one-week recovery times between each phase advance, also led to disruption of the liver circadian epigenome. A model to explain these results is offered.

2018-12-01 | GSE108481 | GEO

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