Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Global transcriptomic changes following N-deprivation in Nannochloropsis oceanica IMET1: Illumina sequencing

ABSTRACT: Limited systems-level understanding of oil synthesis in wild oleaginous algae has hindered the development of microalgal feedstock. Nannochloropsis is a small unicellular microalgae widely distributed in oceans and fresh water. In many large-scale and pilot-scale outdoor cultivation facilities, Nannochloropsis strains have been found to be capable of robust growth when supplied with flue gases, naturally accumulating large quantities of oils in a stationary phase, and exhibiting resistance to environmental contaminants. The rich genomic resources, compact genomes, resistance to foreign DNA invasion, wide ecological adaptation, large collections of natural strains and the demonstrated ability to grow on a large scale suggested Nannochloropsis can serve as research models and platform strains for economical and scalable photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying the robust biomass accumulation and oil production in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal triacylglycerol (TAG) production in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolutiontranscript change for the complete time-courses of nitrogen-depletion-induced TAG synthesis. Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 50 M-BM-5mol photons m-2 s-1) at 25M-bM-^DM-^C and aerated by bubbling with a mixture of 1.5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in nitrogen replete medium (Control condition or C, i.e. N+) and nitrogen deprived medium (N deficiency or N, i.e. N-) with 50M-BM-5mol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 4h, 6h, 12h, 24h and 48h. Three biological replicates of algal cultures were established under each of the above M-bM-^@M-^\CM-bM-^@M-^] (i.e. N+) and M-bM-^@M-^\NM-bM-^@M-^] (i.e. N-) conditions, respectively. In total, 36 samples collected at six time points (3h,4h,6h,12h,24h and 48h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.

ORGANISM(S): Nannochloropsis oceanica

SUBMITTER: Jian Xu

PROVIDER: E-GEOD-42508 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae.

Li Jing J Han Danxiang D Wang Dongmei D Ning Kang K Jia Jing J Wei Li L Jing Xiaoyan X Huang Shi S Chen Jie J Li Yantao Y Hu Qiang Q Xu Jian J

The Plant cell 20140401 4

To reveal the molecular mechanisms of oleaginousness in microalgae, transcriptomic and lipidomic dynamics of the oleaginous microalga Nannochloropsis oceanica IMET1 under nitrogen-replete (N+) and N-depleted (N-) conditions were simultaneously tracked. At the transcript level, enhanced triacylglycerol (TAG) synthesis under N- conditions primarily involved upregulation of seven putative diacylglycerol acyltransferase (DGAT) genes and downregulation of six other DGAT genes, with a simultaneous ele ...[more]

PMID: 24692423

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Project description:Chemostat experiments: Predator-prey dynamics were followed in four replicate chemostats (continuous-flow aquatic culture vessels) supplied with nitrogen-limited sterile medium that was otherwise sufficient in all nutrient constituents (Yoshida et al. 2003; Becks et al. 2010). Three chemostats contained 380 mL of medium, while the fourth, used for our algal gene expression study, contained 3000 mL so as to provide sufficient material for genetic analysis. Brachionus calyciflorus was isolated originally from Milwaukee harbor, Wisconsin, and provided by M. Boraas. Chlamydomonas reinhardtii was obtained from the University of Texas algal culture collection (UTEX 89). Both species reproduced asexually in our chemostat system. Though B. calyciflorus is naturally cyclically parthenogenetic, the rotifers in our stock culture have evolved not to produce males because the bubbling in our chemostats prevents mating; we used only one mating type of Chlamydomonas. Absence of sexual reproduction does not preclude the processes of microevolution (Bell 2009) that we study, and it is commonly accepted that asexual species can evolve (Lenski et al. 1991; Barrett et al. 2005). We used a Chlamydomonas lineage, founded from our original Chlamydomonas stock and then exposed continuously to Brachionus predation for six months in chemostat culture prior to this study during which Chlamydomonas evolved to form clumps (the 'grazed Chlamydomonas' lineage in Becks et al. 2010). We tracked changes in Chlamydomonas gene expression throughout two complete cycles of algal and rotifer abundance and concurrent cycles in algal defense. Algal samples were taken from one chemostat at intervals of approximately every ten days (8 dates total), chosen to capture critical transitions in cell clumping. A sample taken at the start of the experiment from the culture that was used to inoculate the chemostat was the standard against which algae from later samples were compared (i.e., the M-^Sgrazed ChlamydomonasM-^T). To obtain sufficient material for microarray analysis, ca. 1 - 1.5 L algal samples were collected and filtered through a 10-um mesh to exclude rotifers and rotifer eggs. The algal samples of ca. 100 ml of chemostat medium were concentrated by centrifugation and frozen. Samples were shock frozen in liquid nitrogen and transferred to -80C.

Project description:Objective M-bM-^@M-^S Telmisartan, an angiotensin II type 1 (AT1) receptor blocker, and amlodipine, a calcium channel blocker, are antihypertensive agents clinically used as monotherapy or in combination. They exert beneficial cardiovascular effects independently of blood pressure lowering and classic mechanisms of action. In this study, we investigate molecular mechanisms responsible for the off-target effects of telmisartan and telmisartan-amlodipine in endothelial cells (EC), using an unbiased approach. Approach and Results M-bM-^@M-^S In human umbilical vein endothelial cells, microarray analysis of gene expression followed by pathway enrichment analysis and qRT-PCR validation revealed that telmisartan modulates the expression of key genes responsible for cell cycle progression and apoptosis. AmlodipineM-bM-^@M-^Ys effect was similar to control. EC exposed to telmisartan, but not amlodipine, losartan or valsartan, exhibited a dose-dependent impairment of cell growth and failed to enter the S-phase of the cell cycle. Similarly, telmisartan inhibited proliferation in COS-7 cells lacking the AT1 receptor. In telmisartan-treated EC, phosphorylation and activation of Akt as well as MDM2 was reduced, leading to accumulation of p53 in the nucleus, where it represses the transcription of cell cycle promoting genes. Phosphorylation of GSK3M-NM-2 was also reduced, resulting in rapid proteolytic turnover of CyclinD1. Telmisartan induced downregulation of proapoptotic genes and protected EC from serum starvation- and 7-ketocholesterol-induced apoptosis. Conclusions M-bM-^@M-^S Telmisartan exerts antiproliferative and antiapoptotic effects in EC. This may account for the improved endothelial dysfunction observed in the clinical setting. HUVEC were treated with 100 M-BM-5mol/L telmisartan or 5 M-BM-5mol/L amlodipine or both in dimethyl sulfoxide (DMSO) or an equivalent volume of DMSO alone, as control, for 24 hours. Microarray analysis was carried out on two biological replicates per group (total of six samples). See PROTOCOL section for experimental details.

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Dataset Information

Global transcriptomic changes following N-deprivation in Nannochloropsis oceanica IMET1: Illumina sequencing

Publications

Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae.

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