Ontology highlight
ABSTRACT:
PROVIDER: PRJNA655475 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12394639.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The goal of this study was to assess whether low shear-modeled microgravity (LSMMG) effects yeast ,genomic expression patterns using the powerful tool of whole genome microarray hybridization. We determined ,changes in the yeast model organism, Saccharomyces cerevisisae, when grown in LSMMG using the rotating High ,Aspect Ratio Vessel (HARV). A significant number of genes were up- or down-regulated by at least two fold in cells ,that were grown for 5 generations or 25 generations in HARVs. We identified genes in cell wall integrity signaling ,pathways containing MAP kinase cascades that may provide clues to novel physiological responses of eukaryotic ,cells to the external stress of a low-shear modeled microgravity environment. A comparison of the microgravity ,response to other environmental stress response (ESR) genes showed that 26% of the genes that respond ,significantly to LSMMG are involved in a general environmental stress response, while 74% of the genes may ,represent a unique transcriptional response to microgravity. In addition, we found changes in genes involved in ,budding, cell polarity establishment, and cell separation that confirm our hypothesis that exposure to LSMMG ,causes changes in gene transcription resulting in a phenotypic response. The results of the study provide interesting ,clues to potential mechanisms involved in the response to, adaptation to, and survival of eukaryotic cells in a ,microgravity environment and our findings may have important health implications for human spaceflight. Experiment Overall Design: Four conditions are compared with three replicates each: yeast grown in low-shear modeled microgravity (HARV bioreactor) for 5 and 25 generations; yeast grown in a horizontal (non-LSMMG) HARV bioreactor for 5 and 25 generations.
2007-07-07 | E-GEOD-4136 | biostudies-arrayexpress
Project description:Space biomanufacturing using engineered microbes provides a promising approach for sustainable production of biomaterials, pharmaceuticals, and essential metabolites during long-duration space missions. However, microgravity-induced physiological changes have been reported to alter microbial metabolism, substrate transport, and biosynthetic efficiency. In this study, we investigated the effects of microgravity on melanin biosynthesis in non-motile <i>Escherichia coli</i> aboard the International Space Station (ISS). Melanin was chosen as a model biomanufacturing product due to its visible pigmentation, allowing straightforward assessment of production efficiency. Despite expressing a functional tyrosinase enzyme, ISS-grown <i>E. coli</i> exhibited significantly lower melanin production than ground controls. To uncover the underlying mechanisms, differential pulse voltammetry (DPV) analysis confirmed a high extracellular tyrosine concentration in ISS samples, suggesting that substrate was not effectively catalyzed for melanin biosynthesis. Culturing the same strains under Low Shear Modeled Microgravity (LSMMG) conditions in the Rotating Wall Vessel (RWV) bioreactor validated key spaceflight effects, showing reduced melanin production and bacterial viability under low fluid shear conditions. Proteomic profiling of ISS cultures and ground controls identified increased expression of membrane and transport proteins, as well as stress-related proteins involved in oxidative and osmotic stress adaptation. Metabolomic analysis supported these findings, showing an increase in trehalose, a stress response molecule, and a significant decrease in glutathione, indicating perturbed redox homeostasis under microgravity. These findings demonstrate that the microgravity environment of spaceflight affects microbial substrate transport, stress response pathways and cellular metabolism, ultimately impacting biosynthetic efficiency. Understanding these spaceflight-induced metabolic shifts is crucial for optimizing microbial biomanufacturing strategies in extraterrestrial environments.
<p> This complete submission is for the proteomics dataset that is described in the following submitted publication: Hennessa TM, VanArsdale ES, Leary D, Yang J, Davis R, Barrila J, Schultzhaus ZJ, Romsdahl J, Smith AD, Scholes AN, Hervey WJ 4th, Compton JR, Katilie CH, Nickerson CA, Wang Z. Microgravity-Induced Constraints on Melanin Bioproduction: Investigating <i>E. coli</i> Metabolic Responses Aboard the International Space Station. submitted to NPG <i>Microgravity</i> 20 AUG 2025, ACCEPTED 07 JAN 2026.</p>
2025-08-25 | MSV000098933 | MassIVE
Project description:BACKGROUND: Ionizing radiation (IR) can be extremely harmful for human cells since an improper DNA-damage response (DDR) to IR can contribute to carcinogenesis initiation. Perturbations in DDR pathway can originate from alteration in the functionality of the microRNA-mediated gene regulation, being microRNAs (miRNAs) small noncoding RNA that act as post-transcriptional regulators of gene expression. In this study we gained insight into the role of miRNAs in the regulation of DDR to IR under microgravity, a condition of weightlessness experienced by astronauts during space missions, which could have a synergistic action on cells, increasing the risk of radiation exposure. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed miRNA expression profile of human peripheral blood lymphocytes (PBL) incubated for 4 and 24 h in normal gravity (1 g) and in modeled microgravity (MMG) during the repair time after irradiation with 0.2 and 2Gy of γ-rays. Our results show that MMG alters miRNA expression signature of irradiated PBL by decreasing the number of radio-responsive miRNAs. Moreover, let-7i*, miR-7, miR-7-1*, miR-27a, miR-144, miR-200a, miR-598, miR-650 are deregulated by the combined action of radiation and MMG. Integrated analyses of miRNA and mRNA expression profiles, carried out on PBL of the same donors, identified significant miRNA-mRNA anti-correlations of DDR pathway. Gene Ontology analysis reports that the biological category of "Response to DNA damage" is enriched when PBL are incubated in 1 g but not in MMG. Moreover, some anti-correlated genes of p53-pathway show a different expression level between 1 g and MMG. Functional validation assays using luciferase reporter constructs confirmed miRNA-mRNA interactions derived from target prediction analyses. CONCLUSIONS/SIGNIFICANCE: On the whole, by integrating the transcriptome and microRNome, we provide evidence that modeled microgravity can affects the DNA-damage response to IR in human PBL.
2012-04-09 | GSE20120 | GEO
Project description:The goal of this study was to assess whether low shear-modeled microgravity (LSMMG) effects yeast genomic expression patterns using the powerful tool of whole genome microarray hybridization. We determined changes in the yeast model organism, Saccharomyces cerevisisae, when grown in LSMMG using the rotating High Aspect Ratio Vessel (HARV). A significant number of genes were up- or down-regulated by at least two fold in cells that were grown for 5 generations or 25 generations in HARVs. We identified genes in cell wall integrity signaling pathways containing MAP kinase cascades that may provide clues to novel physiological responses of eukaryotic cells to the external stress of a low-shear modeled microgravity environment. A comparison of the microgravity response to other environmental stress response (ESR) genes showed that 26% of the genes that respond significantly to LSMMG are involved in a general environmental stress response, while 74% of the genes may represent a unique transcriptional response to microgravity. In addition, we found changes in genes involved in budding, cell polarity establishment, and cell separation that confirm our hypothesis that exposure to LSMMG causes changes in gene transcription resulting in a phenotypic response. The results of the study provide interesting clues to potential mechanisms involved in the response to, adaptation to, and survival of eukaryotic cells in a microgravity environment and our findings may have important health implications for human spaceflight. Keywords: time course, stress response, budding, microgravity
2006-03-01 | GSE4136 | GEO
Project description:Microarray Profile of Gene Expression during Osteoclast Differentiation in Modeled Microgravity
| PRJNA126713 | ENA
Project description:<b>ABSTRACT:</b> Space biomanufacturing using engineered microbes provides a promising approach for sustainable production of biomaterials, pharmaceuticals, and essential metabolites during long-duration space missions. However, microgravity-induced physiological changes have been reported to alter microbial metabolism, substrate transport, and biosynthetic efficiency. In this study, we investigated the effects of microgravity on melanin biosynthesis in non-motile <i>Escherichia coli</i> aboard the International Space Station (ISS). Melanin was chosen as a model biomanufacturing product due to its visible pigmentation, allowing straightforward assessment of production efficiency. Despite expressing a functional tyrosinase enzyme, ISS-grown <i>E. coli</i> exhibited significantly lower melanin production than ground controls. To uncover the underlying mechanisms, differential pulse voltammetry (DPV) analysis confirmed a high extracellular tyrosine concentration in ISS samples, suggesting that substrate was not effectively catalyzed for melanin biosynthesis. Culturing the same strains under Low Shear Modeled Microgravity (LSMMG) conditions in the Rotating Wall Vessel (RWV) bioreactor validated key spaceflight effects, showing reduced melanin production and bacterial viability under low fluid shear conditions. Proteomic profiling of ISS cultures and ground controls identified increased expression of membrane and transport proteins, as well as stress-related proteins involved in oxidative and osmotic stress adaptation. Metabolomic analysis supported these findings, showing an increase in trehalose, a stress response molecule, and a significant decrease in glutathione, indicating perturbed redox homeostasis under microgravity. These findings demonstrate that the microgravity environment of spaceflight affects microbial substrate transport, stress response pathways and cellular metabolism, ultimately impacting biosynthetic efficiency. Understanding these spaceflight-induced metabolic shifts is crucial for optimizing microbial biomanufacturing strategies in extraterrestrial environments.
<p> This submission is for the metabolomics dataset that is described in the following submitted publication: Hennessa TM, VanArsdale ES, Leary D, Yang J, Davis R, Barrila J, Schultzhaus ZJ, Romsdahl J, Smith AD, Scholes AN, Hervey WJ 4th, Compton JR, Katilie CH, Nickerson CA, Wang Z. Microgravity-Induced Constraints on Melanin Bioproduction: Investigating <i>E. coli</i> Metabolic Responses Aboard the International Space Station. submitted to NPG <i>Microgravity</i> 20 AUG 2025. ACCEPTED 07 JAN 2026.</p>
<p> The complete submission for the proteomics dataset is available at MassIVE accession MSV000098933. </p>
2025-08-25 | MSV000098934 | MassIVE
Project description:Investigating the evolution of Escherichia coli in microgravity offers valuable insights into microbial adaptation to extreme environments. Here the effects of simulated microgravity (SµG) on gene expression of E. coli REL606, a strain evolved terrestrially for 35 years is explored. We evaluated the transcriptomic changes for glucose-limited and glucose-replete conditions over 24 hours which illustrate that SµG increased the expression of stress response and cell membrane-related genes, particularly under glucose-limited conditions. A machine learning model predicted that glucose-limited SµG impacts the cellular membrane, while glucose-replete SµG also inhibits protein synthesis at stationary phase. These findings highlight the transcriptomic and physiological adaptations of E. coli to short term microgravity, offering a foundation for future research into the long-term effects of space conditions on bacterial evolution.
2025-05-13 | GSE284563 | GEO
Project description:Gene expression profiling of human peripheral blood lymphocytes cultured in modeled microgravity
| PRJNA246417 | ENA
Project description:Microgravity effect on C. elegans gene expression was analysed by whole genome microarray. The worms were cultivated under microgravity for 8days in the Japanese Module of the International Space Station.
2012-06-30 | GSE27338 | GEO