Dinoflagellate metagenome
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PROVIDER: PRJNA269082 | ENA |
REPOSITORIES: ENA
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Project description:We compared multiple strains of lab trophozoites to recent clinical isolates. Clinical isolates were grown in xenic media, and maintained many characteristics of the cyst stage of devlopment Keywords: Stage conversion
2007-03-01 | GSE6648 | GEO
Project description:We compared multiple strains of lab trophozoites to recent clinical isolates. Clinical isolates were grown in xenic media, and maintained many characteristics of the cyst stage of devlopment Keywords: Stage conversion E. histolytica trophozoites of three different strains (HM1:IMSS, Rahman, and 200:NIH) and grown under multiple conditions (Long term axenic growth in TYI, Growth in low glucose media, Mouse adapted parasites and in vivo growth in a mouse model) were compared to recent clinical isolates that had grown in xenic culture for 1-8 weeks.
2007-03-01 | E-GEOD-6648 | biostudies-arrayexpress
Project description:Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into role of de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed RNA in Karenia brevis. These isolated fractions were then used for analysis of global de novo transcription by hybridization to a K. brevis microarray. As previous microarray studies indicated that transcripts for pentatricopeptide repeat (PPR) proteins rapidly increased in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of changes in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.
2013-08-01 | GSE46175 | GEO
Project description:Batch cultures of P. donghaiense were maintained in 0.22 filtered and autoclaved seawater (30 psu) with K medium, and grown under cool white fluorescent light at an irradiance of 100 μmol quanta m-2 s-1 with a 14:10 h light: dark cycle at 25 ℃. Tripicated experiments at 19, 22, 25 and 28 ℃ were performed in 2 L acid-washed and autoclaved polycarbonate bottles containing 1.6 L medium. To obtain stable metabolic activity of cells, P. donghaiense at each temperature were cultured and semi-continuously diluted daily for approximately 20 days before samplings.
2022-08-15 | PXD033681 | Pride
Project description:Characterization of bacterial communities associated With toxic Dinoflagellates: pyrodinium bahamense Var. compressum
| PRJNA299717 | ENA
Project description:Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the role of differential mRNA stability in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed/pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 3 days, with a median of 33 hours. Thirteen percent of messages showed a half-life of 3 days, demonstrating their stability throughtout the course of the cell cycle and divison. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes.
2013-08-01 | GSE46174 | GEO
Project description:We report the differential expression of a PAH degrading bacterium in different states of substrate induction. Separate substrate cultivation of the same batch of bacterial isolates; total RNA extraction, processing and sequencing; gene expression analysis using bioinformatics softwares and experimental validation using qRT-PCR.
2013-02-22 | E-GEOD-44536 | biostudies-arrayexpress
Project description:The interaction of an array of volatile organic compounds (VOCs) termed bacterial volatile compounds (BVCs) with plants is now a major area of study under the umbrella of plant-microbe interactions. Many growth systems have been developed to mediate the investigation of these interactions in vitro. However, each of these systems have their benefits and drawbacks with respect to one another and can greatly influence the end-point interpretation of the BVC effect on plant physiology. To address the need for novel growth systems in BVC-Plant interactions our study investigated the use of a passively-ventilated growth system, made possible via Microbox® growth chambers, to determine the effect of BVCs emitted by six bacterial isolates from the genera Bacillus, Serratia and Pseudomonas. Solid-phase microextraction/GC-MS was utilized to determine the BVC profile of each bacterial isolate when cultured in three different growth media each with varying carbon content. 70 BVCs were identified in total with alcohols and alkanes being the most abundant. When cultured in tryptic soy broth, all six isolates were capable of producing 2,5-dimethylpyrazine, however BVC emission associated with this media were deemed to have negative effects on plant growth. The two remaining media types, namely Methyl Red-Voges Proskeur and Murashige and Skoog, were selected for bacterial growth in co-cultivation experiments with Solanum tuberosum cv. ‘Golden Wonder’. The BVC emissions of Bacillus and Serratia isolates cultured on MR-VP induced alterations in the transcriptional landscape of potato across all treatments with 956 significantly differentially expressed genes. Our results indicate that this novel approach to determining BVC-mediated growth effects on plants is a viable alternative and induced differential growth-promotion based on bacterial isolate and the respective media type on which they were cultured. Surprisingly, genes associated with plant defence were often observed to be downregulated in our system whereas genes associated with photosynthesis and plant cell division were upregulated.
2020-10-29 | GSE160297 | GEO
Project description:Reproducibility issues regarding complex in vitro cell culture experiments have been mainly attributed to genetic variations within cell lines. Batch-dependent fetal calf serum variations are well known and also represent relevant influencing factors. However, the molecular constituents mediating such effects remained largely unknown. High resolution mass spectrometry is a powerful tool to identify molecular FCS constituents and investigate their effect on cultured cells. Using a differentiation and inflammatory stimulation protocol on U937 cells we observed FCS batch-dependent variations of secreted cytokines, oxylipins and other inflammatory mediators. In order to detect candidate bioactive molecules contained in FCS, the protein and oxylipin composition of FCS batches was investigated. Remarkably, the protein composition showed some, but much less batch-dependent variation when compared to the oxylipin composition. Efficient uptake of C13-labelled arachidonic acid from medium by U937 macrophages and inflammation-induced release thereof including oxylipin products was evidenced. Balancing out FCS batch-dependent nanomolar concentration differences of two selected oxylipins, 5-HETE and 15-HETE, by spiking experiments, resulted in significant proteome alterations of cultured U937 macrophages indicating PPAR activation. High-resolution microscopy demonstrated HETE-induced formation of peroxisomes, thus independently corroborating the proteome profiling results. In conclusion, the present data demonstrate a strong and previously underappreciated influence of FCS-contained oxylipins on cellular effector functions, thus representing a plausible cause for disturbing reproducibility issues.
2021-06-01 | PXD020617 | Pride
Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.
2023-02-10 | GSE194276 | GEO