Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1262092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR33538570_1.fastq.gz | Fastqsanger.gz | |||
| SRR33538570_2.fastq.gz | Fastqsanger.gz | |||
| SRR33538575_1.fastq.gz | Fastqsanger.gz | |||
| SRR33538575_2.fastq.gz | Fastqsanger.gz |
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Project description:Photoautotrophic cyanobacteria convert CO2 and produce various bioproducts. However, effective cell harvesting from liquid cultivation is a main obstacle. Automatic bio-flocculation provides a potential solution. In a Synechocystis sp. PCC 6803 (Syn) culture, we found that Syn co-flocculated with the natural contaminated fungi (identified as Penicillium sp.) as sphere biomass cluster with space inside, under the treatment of antibiotic erythromycin, but not without erythromycin. The optimized co-cultivation for five days using the initial Syn density of 0.4 OD730, 5 mg/100 ml fresh weight of Penicillium inoculum, and 5 µM EM in the BG11 medium with no organic compounds produced a complete biomass co-flocculation up to 2.0 g/L, equivalent to the atmospheric CO2 capture of 0.6 g/L/d: the 7.9-times biomass level and 7.2-times CO2 capture amount performed by the axenic Syn culture. A major constituent in Syn-Penicillium flocculated biomass is protein contents ranging from 39-61% of dry weight. In addition, increasing EM concentrations (from 0.3 to 10 µM) enlarged the co-flocculate diameter from x to Y and increasing the culture volumes (from 100 to 200-400 mL) altered co-flocculate surface texture from relatively smooth to rough with thorns. This co-flocculation may be further developed for CO2 capture and biomass utilization as amimal feed with a high protein contents. Syn with Penicillium_1; Synechocystis with Penicillium replicate 1 Syn with Penicillium_2; Synechocystis with Penicillium replicate 2 Syn with Penicillium_3; Synechocystis with Penicillium replicate 3 Syn without EM_1; Synechocystis without Erytromycin treatment replicate 1 Syn without EM_2; Synechocystis without Erytromycin treatment replicate 1 Syn without EM_3; Synechocystis without Erytromycin treatment replicate 1 Syn with EM_1; Synechocystis with Erytromycin treatment replicate 1 Syn with EM_2; Synechocystis with Erytromycin treatment replicate 1 Syn with EM_3; Synechocystis with Erytromycin treatment replicate 1 LR_Syn with Penicillium with EM_1; Large star structure of Synechocystis with Penicillium under EM treatment replicate 1 LR_Syn with Penicillium with EM_2; Large star structure of Synechocystis with Penicillium under EM treatment replicate 2 LR_Syn with Penicillium with EM_3; Large star structure of Synechocystis with Penicillium under EM treatment replicate 3 SS_Syn with Penicillium with EM_1; Small smooth structure of Synechocystis with Penicillium under EM treatment replicate 1 SS_Syn with Penicillium with EM_2; Small smooth structure of Synechocystis with Penicillium under EM treatment replicate 2 SS_Syn with Penicillium with EM_3; Small smooth structure of Synechocystis with Penicillium under EM treatment replicate 3
2026-01-26 | GSE296905 | GEO
Project description:Erythromycin-mediated complete co-flocculation between cyanobacterium and Penicillium: the easy-to-harvest co-cultivation without organic compound that increased CO2 fixation and biomass production.
| PRJNA1261913 | ENA
Project description:Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. The fungi in the co-flocculated biomass were isolated and found to consist of five species with the filamentous Purpureocillium lilacinum and Aspergillus protuberus making up 71% of the overall fungal population. The optimal co-cultivation for flocculation was an initial 5 mg (fresh weight) of fungi, an initial cell density of Synechocystis of 0.2 OD730, 10 µM EM, and 14 days of cultivation in 100 mL of BG11 medium with no organic compound. This yielded 248 ± 28 mg/L of the Synechocystis-fungi flocculated biomass from 560 ± 35 mg/L of total biomass, a 44 ± 2 % biomass flocculation efficiency. Furthermore, the EM treated Synechocystis cells in the Synechocystis-fungi flocculate had a normal cell color and morphology, while those in the axenic suspension exhibited strong chlorosis. Thus, the occurrence of the Synechocystis-fungi flocculation was mediated by EM, and the co-flocculation with the fungi helped Synechocystis to alleviate the negative effect of EM. Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. The EM treatment may be applied in the co-culture between other cyanobacteria and fungi to mediate cell bio-flocculation.
2024-05-01 | GSE256452 | GEO
Project description:Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. The fungi in the co-flocculated biomass were isolated and found to consist of five species with the filamentous Purpureocillium lilacinum and Aspergillus protuberus making up 71% of the overall fungal population. The optimal co-cultivation for flocculation was an initial 5 mg (fresh weight) of fungi, an initial cell density of Synechocystis of 0.2 OD730, 10 µM EM, and 14 days of cultivation in 100 mL of BG11 medium with no organic compound. This yielded 248 ± 28 mg/L of the Synechocystis-fungi flocculated biomass from 560 ± 35 mg/L of total biomass, a 44 ± 2 % biomass flocculation efficiency. Furthermore, the EM treated Synechocystis cells in the Synechocystis-fungi flocculate had a normal cell color and morphology, while those in the axenic suspension exhibited strong chlorosis. Thus, the occurrence of the Synechocystis-fungi flocculation was mediated by EM, and the co-flocculation with the fungi helped Synechocystis to alleviate the negative effect of EM. Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. The EM treatment may be applied in the co-culture between other cyanobacteria and fungi to mediate cell bio-flocculation.
2024-05-01 | GSE256451 | GEO
Project description:We demonstrate that low-dose ionizing radiation from X-rays drives metabolic activation in microalgae. We exploited this phenomenon to develop a method for increased lipid yield in stationary phase Chlorella sorokiniana cultures by 25% in just 24 hours, caused by a reproducible metabolic response that includes up-regulation of >30 lipid metabolism genes. This approach avoids the need to modify the strain or cultivation conditions, and does not affect cell viability or biomass.
2024-06-06 | E-MTAB-12288 | biostudies-arrayexpress
Project description:Physiological effects of carbon dioxide and impact on genome-wide transcript profiles were analysed in chemostat cultures of Saccharomyces cerevisiae. In anaerobic, glucose-limited chemostat cultures grown at atmospheric pressure, cultivation under CO2-saturated conditions had only a marginal (<10%) impact on the biomass yield. Conversely, a 25% decrease of the biomass yield was found in aerobic, glucose-limited chemostat cultures aerated with a mixture of 79% CO2 and 21% O2. This observation indicated that respiratory metabolism is more sensitive to CO2 than fermentative metabolism. Consistent with the more pronounced physiological effects of CO2 in respiratory cultures, the number of CO2-responsive transcripts was higher in aerobic cultures than in anaerobic cultures. Many genes involved in mitochondrial functions showed a transcriptional response to elevated CO2 concentrations. This is consistent with an uncoupling effect of CO2 and/or intracellular bicarbonate on the mitochondrial inner membrane. Other transcripts that showed a significant transcriptional response to elevated CO2 included NCE103 (probably encoding carbonic anhydrase), PCK1 (encoding PEP carboxykinase) and members of the IMD gene family (encoding isozymes of inosine monophosphate dehydrogenase Keywords: Dose reponse
2007-08-31 | GSE8900 | GEO
Project description:Limited systems-level understanding of CO2 concentrating mechanism (CCM) and metabolic adaption in response to different CO2-level in wild oleaginous algae has hindered the development of microalgal feedstock and the knowledge of its role in global warming and oceanic acidification. Nannochloropsis are a group of small unicellular microalgae widely distributed in oceans and fresh water, which implies that it plays a crucial role in biogeochemical cycles impinged on global climate change. In addition, Nannochloropsis has been used for flue gas fixation in many large-scale and pilot-scale outdoor cultivation facilities for photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying CCM and metabolic adjustment under different CO2 concentrations in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal CCM and in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolution transcript change for the complete time-courses of different CO2 concentrations.
2019-07-16 | GSE55861 | GEO
Project description:Physiological effects of carbon dioxide and impact on genome-wide transcript profiles were analysed in chemostat cultures of Saccharomyces cerevisiae. In anaerobic, glucose-limited chemostat cultures grown at atmospheric pressure, cultivation under CO2-saturated conditions had only a marginal (<10%) impact on the biomass yield. Conversely, a 25% decrease of the biomass yield was found in aerobic, glucose-limited chemostat cultures aerated with a mixture of 79% CO2 and 21% O2. This observation indicated that respiratory metabolism is more sensitive to CO2 than fermentative metabolism. Consistent with the more pronounced physiological effects of CO2 in respiratory cultures, the number of CO2-responsive transcripts was higher in aerobic cultures than in anaerobic cultures. Many genes involved in mitochondrial functions showed a transcriptional response to elevated CO2 concentrations. This is consistent with an uncoupling effect of CO2 and/or intracellular bicarbonate on the mitochondrial inner membrane. Other transcripts that showed a significant transcriptional response to elevated CO2 included NCE103 (probably encoding carbonic anhydrase), PCK1 (encoding PEP carboxykinase) and members of the IMD gene family (encoding isozymes of inosine monophosphate dehydrogenase Experiment Overall Design: Knowledge on the genome-wide transcriptional response of S. cerevisiae to high CO2 concentrations may provide a deeper insight into the molecular mechanisms of CO2 stress. Such insight is essential to develop metabolic-engineering strategies for improving CO2 tolerance. Furthermore, identification of âsignature transcriptsâ that uniquely respond to CO2 stress may be applicable for diagnosing the CO2 status of industrial fermentations. It has recently been demonstrated that the combination of chemostat cultivation with DNA-microarray-based transcriptome analysis offers a powerful and reproducible approach to identify the transcriptional responses of yeasts to environmental parameters For this reason, in the present study we used chemostat cultures of S. cerevisiae to quantify the effect of CO2 on respiring and fermenting cells, and to determine the genome-wide transcriptional responses of this yeast to high CO2 concentrations.
2008-06-16 | E-GEOD-8900 | biostudies-arrayexpress
Project description:Daphnia infochemicals can induce defensive responses in microalgae Scenedesmus spp., including colony formation and flocculation. We investigated the phenomenon using a combination of microalgal biology, physiological ecology, and quantitative isobaric tagging (iTRAQ) proteomics. We have discovered that flocculation as a defense response occurs at the early ‘alarm’ phase and requires increased energy resources, with an important role proposed in cysteine synthesis. It appears to be initially stimulated by the production of an extracellular matrix (mainly composed ofby polysaccharides and fatty acids), and later sustained at the ‘acclimation’ stage through Mitogen-activated protein kinase (MAPK) signalling cascades. Defensive strategies leading to colony formation required investment into fatty acids metabolism, to ensure the accurate separation of membranes during cell division. Furthermore, higher energy demands were required at the alarm phase which subsequently decreased at the acclimation stage, thus suggesting a trade-off between colony formation and support of floc form.
2020-05-06 | PXD014153 | Pride
Project description:Methicillin-resistant Staphylococcus aureus (MRSA) remains a global health threat with an over 14% fatality rate, in case of invasive infection, in 2011. Multi-drug resistance is the main reason for the failure of therapy. Use of antimicrobial drug combinations with synergistic effect is increasingly seen as a critical strategy to combat multi-drug resistant pathogens such as MRSA. However, the mechanism of synergistic effect has yet been systematically studied. In this work, we investigated a new erythromycin derivative, SIPI-8294, which has been demonstrated to have synergistic effect with oxacillin against MRSA, unlike its parent compound erythromycin. To obtain insights into the mechanism for the synergistic effect, label-free quantitative proteomics was employed. Cultured MRSA was exposed to sub-inhibitory doses of oxacillin, SIPI-8294, erythromycin, and combinations of SIPI-8294/oxacillin and erythromycin/oxacillin to reveal the global proteome responses to drug treatment. Results showed that 200 proteins were differentially expressed in SIPI-8294/oxacillin-treated cells. Among these proteins, the expression levels of penicillin binding protein 2a and β-lactamase, two proteins mainly responsible for oxacillin resistance, were four times lower in the SIPI-8294/oxacillin treatment group than in the erythromycin/oxacillin treatment group. Quantitative real-time PCR analysis also revealed similar trends at the transcription level. These results suggest that the synergistic mechanism may be related to interference with the known oxacillin resistance mechanism. The data also provided some evidence that the combination of SIPI-8294 and oxacillin appears to impact oxidation-reduction homeostasis and cell wall biosynthesis.
2022-03-01 | PXD001494 | Pride