Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1172573 | ENA |
REPOSITORIES: ENA
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Project description:Gas fermentation of CO₂ and H₂ is an attractive means to sustainably produce fuels and chemicals. Clostridium autoethanogenum is a model organism for industrial CO-to-ethanol and presents an opportunity for CO₂-to-ethanol processes. As we have previously characterized its CO₂/H₂ chemostat growth, here we use adaptive laboratory evolution (ALE) with the aim of improving growth with CO₂/H₂. Seven ALE lineages were generated, all with improved specific growth rates. Developed with 2% CO supplementation of CO₂/H₂, Evolved lineage D has the highest ethanol/acetate of ALE lineages when fermenting CO₂/H₂. Chemostat comparison against the parental strain shows no change in acetate or ethanol production, while Evolved D could achieve a higher maximum dilution rate. Complete multi-omics analyses at steady-state revealed that although Evolved D has widespread proteome changes, intracellular metabolites prevent phenotype shifts. Yet, we observe numerous insights to CO₂/H₂ metabolism via these multi-omics results and link these to mutations, suggesting novel targets for metabolic engineering.
2024-05-09 | PXD048143 | Pride
Project description:Gas fermentation of CO₂ and H₂ is an attractive means to sustainably produce fuels and chemicals. Clostridium autoethanogenum is a model organism for industrial CO-to-ethanol and presents an opportunity for CO₂-to-ethanol processes. As we have previously characterized its CO₂/H₂ chemostat growth, here we use adaptive laboratory evolution (ALE) with the aim of improving growth with CO₂/H₂. Seven ALE lineages were generated, all with improved specific growth rates. Developed with 2% CO supplementation of CO₂/H₂, Evolved lineage D has the highest ethanol/acetate of ALE lineages when fermenting CO₂/H₂. Chemostat comparison against the parental strain shows no change in acetate or ethanol production, while Evolved D could achieve a higher maximum dilution rate. Complete multi-omics analyses at steady-state revealed that although Evolved D has widespread proteome changes, intracellular metabolites prevent phenotype shifts. Yet, we observe numerous insights to CO₂/H₂ metabolism via these multi-omics results and link these to mutations, suggesting novel targets for metabolic engineering.
2024-05-09 | PXD048075 | Pride
Project description:A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intended to mimic industrial processes.
2023-02-21 | GSE212531 | GEO
Project description:Bordetella pertussis is the bacterial causative agent of whooping cough, a serious respiratory illness. An extensive knowledge on its virulence regulation and metabolism is a key factor to ensure pertussis vaccine manufacturing process robustness. The aim of this study was to refine our comprehension of B. pertussis physiology along the fermentation process. A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intending to mimic industrial processes. Putative cysteine and proline starvations were respectively observed at the beginning of the exponential phase (from 4h to 8h) and during the exponential phase (18h45). As revealed by multi-omics analyses, the proline starvation induced major molecular changes, including a transient metabolism with internal stock consumption. In the meantime, growth and specific total PT, PRN and Fim2 antigen productions were negatively affected. Interestingly, the master virulence-regulating two-component system of B. pertussis (BvgASR) was not evidenced as the sole virulence regulator in this in vitro growth condition. Indeed, novel intermediate regulators were identified as putatively involved in the expression of some virulence-activated genes (vags). Such longitudinal multi-omics analysis applied to B. pertussis fermentation process emerges as a powerful tool for characterization and incremental optimization of vaccine antigen production.
2023-03-11 | PXD039615 | Pride
Project description:DNA methylation array data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. DNA was extracted from suction blisters taken from the volar forearms of each subject, bisulfite converted, and profiled using Illumina Infinium HumanMethylation450 BeadChip arrrays.
2020-07-24 | E-MTAB-8992 | biostudies-arrayexpress
Project description:DNA methylation array data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. DNA was extracted from suction blisters taken from the volar forearms of each subject, bisulfite converted, and profiled using Illumina Infinium MethylationEPIC BeadChip arrrays.
2020-07-24 | E-MTAB-8993 | biostudies-arrayexpress
Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress
Project description:Investigation of lung adenocarcinoma (LUAD) and breast cancer cells cultured in either a nutrient-rich or -restricted culture conditions trough a multi-omics approach, including transcriptomics, to explore the molecular changes underlying the transition from 2D to 3D cultures.
2023-04-05 | GSE215235 | GEO
Project description:Whole transcriptome sequencing data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. RNA was extracted from suction blisters taken from the volar forearms of each subject, cDNA converted and then sequenced on an Illumina HiSeq 2500 (single-end, 50 bp) to an approximate sequencing depth of 100 million reads per sample.
2020-07-24 | E-MTAB-8995 | biostudies-arrayexpress