Time course of glycine addition or withdrawal
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE1554 | GEO | 2004/07/17
SECONDARY ACCESSION(S): PRJNA89957
REPOSITORIES: GEO
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Project description:+Gly 20, 40, 80: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) and t=0 time point samples were harvested (250 ml). The remainder of the medium was supplemented with 10 mM glycine incubated at 30oC and samples (250 ml) harvested at 20, 40 and 80 minutes. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. -Gly 20, 40, 80: Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) supplemented with 10 mM glycine and t=0 time point samples were harvested (250 ml). The remainder of the medium was filtered and the cells were rapidly resuspended in 750 ml of pre-warmed B minimal medium, incubated at 30oC and samples (250 ml) harvested at 20, 40 and 80 minutes. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Keywords: time-course
2010-10-08 | E-GEOD-1554 | biostudies-arrayexpress
Project description:Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) with or without supplementation with 10 mM glycine and harvested. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Arrays compared expression of Gly- cells to the Gly+ controls. Strain BY4741 was the wild type and several deletion strains were also used. Keywords: parallel sample
2004-07-17 | GSE1553 | GEO
Project description:Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) with or without supplementation with 10 mM glycine and harvested. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Arrays compared expression of Gly- cells to the Gly+ controls. Strain BY4741 was the wild type and several deletion strains were also used. Keywords: parallel sample
2004-07-17 | E-GEOD-1553 | biostudies-arrayexpress
Project description:In this study, the effect of nitroprusside on protein expression of the model sulfate reducing bacterial isolate (Desulfovibrio vulgaris Hildenborough) was investigated. Three different experiments were done with different exposure time to nitroprusside (30 min, 1 hour, and 3 hours). In each experiment, the culture was grown in quadruplet of serum bottles containing 40 ml complex medium (Postgate medium B) under anaerobic condition at 30oC. At mid-log growth phase, each of the quadruplet culture was divided into two (20 ml each) and nitroprusside (0.25 mM) was added to one of each bottle while the other bottles were used as controls. After 30 min, 1 hour, and 3 hours of exposure to nitroprusside, the culture (1 ml) was pelleted and used for proteomic analysis.
2018-05-17 | PXD007623 | Pride
Project description:Purpose: To understand how D654Y mutated RpoB affect gene expression under either normal or osmotic stress conditions in Escherichia coli . Methods: RNA-seq libraries were constructed for four samples, including (I) The parental strain Suc-T110 grown at normal condition (5%w/v glucose); (II)RpoB mutant RpoBD645Y [Suc-T110::rpoB (D654Y), RNA-seq library named NZ-502] grown at normal condition;(III) Suc-T110 grown at osmotic stress condition(12%w/v glucose);(IV) NZ-502 grown at osmotic stress condition. For preparation of RNA samples, Fresh colonies were picked from New NBS mineral salts plates containing 20 g liter-1 glucose, inoculated into 250 ml flasks containing 30 ml NBS mineral salts medium with 20 g liter-1 glucose, and grown at 37°C and 250 rpm for 12 h. Cultures were then transferred to a 500 ml fermentation vessel containing 250 ml NBS mineral salts medium with either 5%w/v or 12%w/v glucose. After 48 h, 1 ml culture was harvested by centrifugation, frozen in liquid nitrogen and sent to Beijing Genomics Institute (BGI, Shenzhen, China). The four 90-nt paired-end RNA-seq libraries were generated commercially at Beijing Genomics Institute by using the HiSeq™ 2000 platform. Sequencing data was handled essentially with Bowtie2, NOIseq. Expression levels are presented as Reads Per Kilobase of transcript per Million mapped reads (RPKM). Results: we first comparative accessed expression levels of Suc-T110 and NZ-502 under normal condition. Among the 4200 predicted genes, 128 genes were found altered their expression in NZ502 compared with Suc-T110; with 38 targets specific up-regulated while 90 targets down-regulated. Genes engaged in biological function of amino acid metabolism (P-value=4.60E-05) were significantly enriched among in induced gene set. Under osmotic stress condition, 244 differential expressed genes were identified in NZ-502 when compared with Suc-T110, with 132 targets specific up-regulated while 112 targets down-regulated, Functional enrichment of 132 up regulated genes showed the most significantly enriched physiological function of NZ-502 upon hyperosmotic stress was associated with carbon source transportation (FunCat term: 20.01.03 C-compound and carbohydrate transport, P-value=9.51E-05), which containing a group of genes encoding diverse sugar transporters. Conclusions: Transcriptome profiling suggested that derepression of sugar transporters might be the primary cause for NZ-502 to resist osmotic stress.
2017-02-04 | GSE84769 | GEO
Project description:E.coli ATCC 25922 was overnight grown in 10 ml LB and passaged for 3 h with 1:50 dilution in fresh LB. Treated with tavaborole alone (80 μg/ml, labeled ‘A’) or tavaborole plus amikacin (80 μg/ml +40 μg/ml, labeled ‘AK’) for 6 h, cells were washed in PBS and harvested by centrifugation at 4,000 g, 8 min. After liquid nitrogen flash freezing, cells were stored at -80 °C and transported to company for following experiments
2023-03-10 | PXD033907 | Pride
Project description:Wild type and hemA strains of Escherichia coli MG1655 were grown under anaerobiosis in batch culture in custom-made, stirred (200 rpm) 250 ml mini-fermenter vessels at 37 °C during continuous sparging with 100 % nitrogen gas. Cells were grown in defined medium (pH 7.0) containing 0.5 % glucose as the sole and limiting source of energy and carbon. The medium was supplemented with 0.1 % casamino acids and 5 % LB to support the growth of the hemA mutant. For maintenance of the hemA mutation, 50 mg/ml kanamycin were added to cultures of the heme-deficient mutant only. CORM-3 (final concentration of 100 uM) was added to wild type and mutant cultures at an OD600 of 0.2. iCORM-3 (final concentration of 100 uM) was added to only mutant cultures at an OD600 of 0.2. Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and at consecutive time-points thereafter (10, 20, 40, 60 and 120 min) for microarray analysis. Cells were harvested directly into phenol:ethanol to stabilise RNA and total RNA was purified using Qiagen’s RNeasy Mini Kit, according to the manufacturer's instructions.
2015-04-01 | GSE55097 | GEO
Project description:We probed the mechanism of cross-regulation of osmotic and heat stress responses by characterizing the effects of high osmolarity (0.3M vs. 0.0M NaCl) and temperature (43oC vs. 30oC) on the transcriptome of Escherichia coli K12 using E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures). Total RNA was extracted using a hot phenol-chloroform method. cDNA synthesis, fragmentation and labeling, and washing and scanning of E. coli GeneChip Arrays were performed according to the instructions of the manufacturer (Affymetrix Technical Manual, Affymetrix, Inc., USA). Labeled cDNA was hybridized to E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures) of each condition. A number of genes in the SoxRS and OxyR oxidative stress regulons were up-regulated by high osmolarity, high temperature, and/or by the combination of both stresses. This result could account for cross-protection of osmotic stress against oxidative stress. The trehalose biosynthetic genes were induced by both stresses, in accord with the proposed protective role of this disaccharide against thermal and oxidative damage. Experiment Overall Design: E. coli K12 strain NCM3722 cultures were grown with aeration in K medium containing 10 or 20 mM glucose. To impose osmotic stress, the osmolarity of the medium was increased to 0.64 osm by supplementation with 0.3 M NaCl. Because E. coli is a methionine auxotroph above 42oC the K medium cultures were supplemented with 0.5 mM methionine. Glycine betaine (GB) was added to the high osmolarity media to a final concentration of 1 mM. Cells taken from a single colony on LB agar were inoculated into 1ml liquid LB and grown to saturation at 37oC, then 0.05 ml were inoculated into i) K medium, 0.5 mM methionine, 10 mM glucose; ii) K medium, 0.5 mM methionine, 10 mM glucose, 0.3 M NaCl; and iii) K medium, 0.5 mM methionine, 10 mM glucose, 0.3 M NaCl, 1 mM GB. The cultures were grown to saturation at 30oC and 43oC, and sub-cultured once into the same medium and grown at the same temperatures as before. Exponentially growing cells form these cultures were then inoculated into Erlenmeyer flasks (starting OD600nm 0.05) containing 40 ml of the same medium, and incubated in the same salt and temperature conditions as used previously, except that the glucose concentration was increased to 20 mM. When the cells reached OD600nm of 0.4-0.5 (~3 doublings), 25 ml were added to a 2.5 ml mixture of cold 95% ethanol and 5% phenol to preserve RNA. The cells were cooled briefly on ice, immediately harvested by centrifugation (4oC), and the pellet was frozen on dry ice. The six different growth conditions used were: C1 - 30oC, no NaCl; C2: 30oC, 0.3 M NaCl; C3: 30oC, 0.3 M NaCl, 1 mM GB; C4: 43oC, no NaCl; C5: 43oC, 0.3 M NaCl; C6: 43oC, 0.3 M NaCl, 1 mM GB.
2009-01-14 | E-GEOD-7656 | biostudies-arrayexpress
Project description:The influence of substrate composition on extracellular protein production was evaluated in media containing glucose, lodgepole pine or aspen as carbon sources. Common to all media, basal salts contained, per liter, 2g NH4NO3, 2g KH2, 0.5 g MgSO4·7H2O, 0.1 g CaCl2·2H2O, 1 mg thiamine hydrochloride and 1 mL trace element solution (Teknova, T1001). Aspen and pine were added to 5 g per liter, while the glucose cultures received 2.5 g per liter. All cultures contained 100 mL media in 500 ml Erlenmeyer flasks and, following inoculation with macerated mycelium, incubated on a rotary shaker (100 RPM) at 24°C. Aspen (Populus grandidentata) and lodgepole pine (Pinus contorta) were Wiley milled and sieved to one mm mesh prior to inoculation. Triplicate cultures were harvested after 5 and 10 days.
2023-09-15 | PXD045363 | Pride
Project description:The influence of substrate composition on extracellular protein production was evaluated in media containing glucose, lodgepole pine or aspen as carbon sources. Common to all media, basal salts contained, per liter, 2g NH4NO3, 2g KH2, 0.5 g MgSO4·7H2O, 0.1 g CaCl2·2H2O, 1 mg thiamine hydrochloride and 1 mL trace element solution (Teknova, T1001). Aspen and pine were added to 5 g per liter, while the glucose cultures received 2.5 g per liter. All cultures contained 100 mL media in 500 ml Erlenmeyer flasks and, following inoculation with macerated mycelium, incubated on a rotary shaker (100 RPM) at 24°C. Aspen (Populus grandidentata) and lodgepole pine (Pinus contorta) were Wiley milled and sieved to one mm mesh prior to inoculation. Triplicate cultures were harvested after 5 and 10 days.
2023-09-15 | PXD045112 | Pride