RNA-seq experiment of the amoeboflagellate Orciraptor agilis feeding on Mougeotia sp.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500, Illumina HiSeq 4000
ORGANISM(S): Mougeotia sp. CCAC 3626
SUBMITTER: Jennifer Gerbracht
PROVIDER: E-MTAB-11291 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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.
2012-03-20 | E-MEXP-3562 | biostudies-arrayexpress
Project description:Peptides were identified during degradation of the diatom Thalassiosira weissflogii with and without the use of the enzyme trypsin. This allows comparison of protein degradation occurring within the experiment (no trypsin added; peptides already present due to in situ degradation) and the protein still available for future degradation (peptides released from protein when trypsin is added during analysis). Over the 12-day degradation experiment 31% of the particulate organic carbon was depleted and there was no preferential degradation of the overall protein pool. However, there was distinct differentiation in the cellular location, secondary structure and modifications of the peptides that were either degraded or remained. During the initial period of rapid algal decay and bacterial growth, intracellular components from the cytoplasm were selectively consumed, resulting in the accumulation of membrane-associated proteins and peptides in the detrital pool. Accompanying this was an increase in the importance of membrane-bound ɑ-helix motifs. At the end of the 12 day experiment, the natural bacterial assemblage was focusing on degradation of membrane-associated proteins, which was the dominant source of peptides in both the residual pool (released by trypsin) and the actively degraded pool (no trypsin added). Methylated arginine, a post-translationally modified amino acid that is produced within the diatom prior to senescence, is found in high amounts within the detrital peptide pool, suggesting a link between in-cell modification and resistance to immediate degradation. Another modification - asparagine deamidation - appears to occur during degradation and deamidated peptides also accumulate within the detritus. The bacterial community decomposing the algal material was rich in proteobacteria, and employed a growth approach focusing on accumulation of solubilized material across their membranes and on DNA replication. At this early stage of diagenesis, no changes in bulk amino acids (THAA) were observed, yet a peptidomic approach allowed us to observe the differential changes in diatom protein preservation by discriminating between intracellular location, secondary structure, and modifications status.
2021-12-20 | PXD027843 | Pride
Project description:Total RNA was extracted from Anabaena 7120, hetZ mutant and hetP mutant at 24 h after nitrogen stepdown with two independent biological replicates. To maintain the integrity of coding RNAs, total RNA were sequenced without ribosomal RNA elimination. Strand-specific RNA-Seq libraries were prepared and sequenced using the Illumina HiSeq 2500 sequencing instrument to generate paired-end reads with length of 125 bp.
2018-02-19 | E-MTAB-6459 | biostudies-arrayexpress
Project description:This study aims at investigating the link between internalized inorganic or methyl Hg and the global expression of genes, obtained by high-throughput sequencing (RNA-Seq), in the microalga Chlamydomonas reinhardtii. Algal cells were exposed two hours in a simplified artificial medium spiked with series of inorganic Hg concentrations (0.1, 1, 100 nM Hg) or series of methyl Hg concentrations (0.05, 0.5, 5, 50 nM CH3Hg). Three biological replicates were assessed for each of the 8 tested conditions: Control, 3 Hg concentrations, 4 CH3Hg concentrations.
2017-06-27 | E-GEOD-65109 | biostudies-arrayexpress
Project description: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.
2014-05-14 | E-GEOD-42508 | biostudies-arrayexpress
Project description:The Zygnematophyceae are the closest algal relatives of land plants and hence interesting to understand land plant evolution. Species of the genus Serritaenia have an aerophytic lifestyle and form colorful, mucilaginous capsules, which surround the cells and block harmful solar radiation. Under laboratory conditions the production of this “sunscreen mucilage” can be induced by ultraviolet B radiation. The present dataset reveals insights into the cellular reaction of this alga to UV radiation (a major stressor in terrestrial habitats) and allows for comparisons with other algae and land plants to draw evolutionary conclusions.
2024-03-12 | E-MTAB-13832 | biostudies-arrayexpress
Project description:Microalgae are promising production platforms for the cost-effective production of recombinant proteins. We have recently established that the red alga Porphyridium purpureum provides superior transgene expression properties, due to the episomal main- tenance of transformation vectors as multicopy plasmids in the nucleus. Here, we have explored the potential of Porphyridium to synthesize complex pharmaceutical proteins to high levels. Testing expression constructs for a candidate subunit vaccine against the hepatitis C virus (HCV), we show that the soluble HCV E2 glycoprotein can be produced in transgenic algal cultures to high levels. The antigen undergoes faithful posttranslational modification by N-glycosylation and is recognized by conformationally selective antibodies, suggesting that it adopts a proper antigenic conformation in the endoplasmic reticulum of red algal cells. We also report the experimental determina- tion of the structure of the N-glycan moiety that is attached to glycosylated proteins in Porphyridium. Finally, we demonstrate the immunogenicity of the HCV antigen produced in red algae when administered by injection as pure protein or by feeding of algal biomass.
2024-05-21 | PXD052401 | Pride
Project description:Transcriptomic study for the response of Ectocarpus siliculosus to mild copper stress (250 µg L-1 CuCl2) after 4h and 8h of exposure
2014-03-10 | E-MTAB-1286 | biostudies-arrayexpress
Project description:A unique, lymphoid tissue located adjacent to the eye of the chicken, the Harderian gland is assumed to have critical immune functions, but prior to the current study, its transcriptome had never been analyzed. This study aimed to characterize differential responses between the relatively resistant (Fayoumi) and susceptible (Leghorn) chicken lines when challenged with a high titered lentogenic Newcastle Disease Virus (NDV) strain via the eyes and nares at three weeks of age. The Harderian gland was collected from challenged and non-challenged birds from each line at 2, 6, and 10 days-post-infection (dpi) (n=47). High quality RNA was isolated, used for cDNA library construction, and sequenced on the HiSeq2500.
2018-05-01 | E-MTAB-6038 | biostudies-arrayexpress
Project description:Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature. 16 samples with 3 biological replicates each.
2014-03-31 | E-GEOD-37673 | biostudies-arrayexpress