Global gene expression of Ruegeria pomeroyi strain DSS3 in response to glucose, ammonium, phosphate, or sulfate limitation
ABSTRACT: We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation. Overall design: A total of 14 mRNA samples were hybridized to the arrays (three biological replicates from glucose, ammonium, phosphate, or sulfate limitation and one technical replicate each for ammonium or sulfate limitation)
Project description:We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation. A total of 14 mRNA samples were hybridized to the arrays (three biological replicates from glucose, ammonium, phosphate, or sulfate limitation and one technical replicate each for ammonium or sulfate limitation)
Project description:We used the previously designed oligonucleotide microarrays (Bürgmann et al., 2007, Environmental Microbiology, 9: 2742-2755) to detect the mRNA transcripts of R. pomeroyi DSS-3 when the cells were cultured under steady-state conditions limited with ammonium (NH4Cl, 0.26 mM) but with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methylphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM), or during ammonium excess (NH4Cl, 2.8 mM) but were limited with potassium phosphate (KH2PO4, 9.2 μM). A total of 13 microarray hybridizations were performed: three biological replicates each from ribose phosphate, methylphosphonate, or potassium phosphate excess growth regimes, three biological replicates from potassium phosphate limited growth regime, and one technical replicate for the potassium phosphate excess growth regime. Data for the technical replicates were averaged and combined, resulted in a total of 12 samples.
Project description:Next generation sequencing was used to assess transcriptome changes in haploid U. maydis wild type and mutant strains grown under nitrogen-replete and low ammonium media. Overall design: Wild type and mutant strains were grown for 48 hours at 26 C, in microarray media ((6.25% Holliday Salt Solution (Holliday, 1974), 1% glucose, and 2% agar) with either 30 mM Glutamine/50 mM Ammonium sulfate (Hi) or 50 uM Ammonium sulfate (Lo)
Project description:S. cerevisiae cells (homozygous deletion mutants of BY4743) grown in chemostats, sampled at steady state. Glucose and ammonium limitation, dilution rates 0.1 and 0.2 hr<sup>-1</sup>, gene deletions HO and HAP4 applied.
Project description:In the present study the effect of phosphorus (P) limitation was investigated in the microalgae Nannochloropsis oceanica. Algal cultures were analysed for transcriptomic and lipidomic changes during P-limited growth, with sample time points: 24h, 48h, 53h, 58h and 70h. The transcriptome data identified unique P acquiring genes and the results were also supported by corresponding changes in the lipidome dataset, which showed a lipid class shift from phospholipids to phosphorus-free lipids under P-limitation. During the exponential growth phase a gradual 6-fold reduction of the cellular P level induced RNA transcripts encoding proteins acquiring P from inorganic and organic sources. For this process 6 novel purple acid phosphatases and 5 unique Pi transporters were identified. Additionally, increased gene expression of 2 triose-phosphate transporters (TPTs) indicated the importance of the carbon-to-phosphorus balance for the plastidial anabolic processes. Phospholipid degradation was shown to be an early response to P limitation, by overexpression of sets of 2 novel glycerophosphoryl diester phosphodiesterases (GDPDs), and 3 patatin-like phospholipases of type A. To compensate for phospholipid degradation, the transcriptome and lipidome level showed increased synthesis of sulfoquinovosyl diacylglycerol (SQDG), and diacylglyceroltrimethylhomoserine (DGTS). Phosphorus limitation triggered the lipid class shift in both the exponential growth phase and the triacylglycerol (TAG) accumulation period to release P and increase the organic C:P ratio. Overall design: Axenic pre-cultures of Nannochloropsis oceanica CCMP1779 were grown in f/2 medium without silica in three 2 L Nalgene optically clear flasks (Thermo Fisher Nalgene®) under constant light (350 µmoL photons m-2 s-1), at 23°C. The Nalgene optically clear flasks were aerated with sterile-filtered air. The pre-cultures were grown to the exponential growth phase (OD750nm= 0.40, ~8*106 cells / mL), mixed, harvested, and washed with sterile seawater by centrifugation (4,700xg, 20 min). The experimental cultures were inoculated to an OD750nm of 0.06 (~2.5*106 cells / mL) in either f/2 medium without silica (36.38 μM PO43-, +P cells) or f/2 medium without silica with a reduced phosphate concentration (2.79 μM PO43-, -P cells). Three biological replicates of the algal cultures were established for each of the mentioned growth conditions. Samples of phosphate depleted cells were harvested at 24h, 48h, 54h, 58h and 72h, while samples from phosphate replete cultures were harvested after 24h.
Project description:Response of Saccharomyces cerevisiae to Ammonium, L-alanine, or L-glutamine Limitation. The protrotophic laboratory strain CEN.PK113-7D (MAT a) was grown in laboratory fermentors with a working volume of 1 litre at dilution rate (D) of 0.20 per hour (in triplicate for each nitrogen limited condition). At steady state, samples from each of the 12 continuous cultures were taken and cooled below 2 degree C within ten seconds by mixing 40% sample and 60% crushed ice.
Project description:Responses of Pelagibacterales strains to phosphate limitation Overall design: Batch cultures of two different strains of P. ubique (HTCC1062 and HTCC7211) were grown in a defined artificial seawater media. Biological replicates of each strain were given no phosphate amendment, and three other cultures received an excess concentration of phosphate. Cultures were harvested for microarray analyses over a time course for the purpose of observing differences in gene expression related to phosphate limitation.
Project description:Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples. Overall design: Two samples cultured in minimum media with abundant ammonium (MM) or minute ammonium (MM-N)
Project description:Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for hydrogen, phosphate, or leucine were compared to determine the regulatory response to hydrogen limitation. This was done by comparing hydrogen limited cultures to both leucine limited and phosphate limited cultures. Slow and rapid growing samples limited for either hydrogen or phosphate were compared to determine the regulatory effects of growth rate. Keywords: archaea, hydrogen, leucine, phosphate, nutrient limitation, growth rate, methanogen Overall design: Four biological replicates of hydrogen limited cells grown in chemostats were compared to four biological replicates of leucine limited and phosphate limited chemostat cultures. For growth rate comparisons, two sets were compared, each with three biological replicates of cultures grown at slow and rapid growth rates in chemostats. One set was limited by hydrogen availability at both growth rates, the other by phosphate availability. Each comparison was conducted with a dye swap and each contained two copies of the array, yielding 4 technical replicates for each biological replicate. This yielded a total of 16 replicates for the hydrogen versus leucine and hydrogen versus phosphate comparisons and 12 replicates each for the growth rate comparisons for both hydrogen and phosphate limitation. For growth rate comparisons under phosphate limited conditions a second scanning was done at lower gain set so that no spot reached saturation.