Sequence_data_FEMS_Krause_2015
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ABSTRACT:
PROVIDER: PRJEB11175 | ENA |
REPOSITORIES: ENA
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Project description:Rice paddies contribute substantially to atmospheric methane (CH4) and these emissions are expected to increase as the need to feed the human populationgrows. Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduced cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over the growth period compared with controls. Genome-resolved metatranscriptomic data from rhizosphere soils reveal lower ratios of gene activities for CH4 production versus consumption, decrease in activity of H2-producing genes, and increase in bacterial H2 oxidation pathways in the PSY genotypes. Metabolic modeling using metagenomic and metabolomic data predicts elevated levels of H2 oxidation and suppressed H2 production in the PSY rhizosphere. The H2- oxidizing bacteria have more genes for utilization of gluconeogenic acids than H2- producing counterparts, and their activities were likely stimulated by the observed enrichment of gluconeogenic acids (mostly amino acids) in PSY root exudates. Together these results suggest that decreased CH4 emission is due to the reduction of H2 available for hydrogenotrophic methanogenesis. The combination of rice phenotypic characterization, microbiome multi-omic analysis, and metabolic modeling described here provides a powerful strategy to discover the mechanisms by which specific plant genotypes can alter biogeochemical cycles to reduce CH4 emissions.
The work (proposal:https://doi.org/10.46936/10.25585/60008481) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-11-06 | MSV000096316 | MassIVE
Project description:Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly being studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker, pmoA, were found to vary quantitatively with respect to methane oxidation rates in model aerobic methanotroph, Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per cell pmoA mRNA transcript levels strongly correlated with per cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). Additionally, genome-wide expression data (RNA-seq) were used to explore transcriptomic responses of steady state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response.
2021-11-17 | GSE188821 | GEO
Project description:Previous studies have shown that methane (CH4) has promoting roles in the adventitious root (AR) and lateral root formation in plants. However, whether CH4 could trigger the bulblet formation in scale cutting of Lilium davidii var. unicolor has not been elucidated. To gain insight into the effect of CH4 on the bulblet formation, different concentrations (1%, 10%，50% and 100%) of methane-rich water (MRW) and distilled water were applied to treat the scale cuttings of Lilium. We observed that treatment with 100% MRW obviously induced the bulblet formation in scale cuttings. To explore the mechanism of CH4-induced the bulblet formation, the transcriptome of scales was analyzed. A total of 2078 differentially expressed genes (DEGs) were identified. The DEGs were classified into different metabolism pathways, especially phenylpropanoid biosynthesis, starch and sucrose metabolism and plant signal transduction. Of these, approximately 38 candidate DEGs involved in the plant signal transduction were further studied. In addition, the expression of AP2-ERF/ERF, WRKY, GRAS, ARF and NAC transcription factors were changed by MRW treatment, suggesting their potential involvement in bulblet formation. As for hormones, exogenous IAA, GA and ABA could indue the bulblet formation. Additional experiments suggested that MRW could increase the endogenous IAA, GA, and JA levels, but decrease the levels of ABA during bulblet formation, which showed that higher IAA, GA, JA levels and lower ABA content might facilitate bulblet formation. In addition, the levels of endogenous hormone were consistent with the expression level of genes involved in phytohormone signal transduction. Overall, this study has revealed that CH4 might improve the bulblet formation of cutting scales in Lilium by regulating the expression of genes related to phytohormone signal transduction and transcription factors, as well as by changing the endogenous hormone levels.
2021-03-08 | GSE168030 | GEO
Project description:The increasing consumption of high-fat western foods combined with a lack of exercise is a major contributor to the burden of obesity in humans. Aerobic exercise such as running is known to provide metabolic benefits, but how the over-consumption of a high fat diet (HFD) and exercise interact is not well characterized at the molecular level. Here, we examined the plasma proteome in mice for the effects of aerobic exercise as both a treatment and as a preventative regime for animals on either HFD or a healthy control diet. This analysis detected large changes in the plasma proteome induced by the HFD intervention, such as increased abundance of SERPINA7, ALDOB, APOE, and down-regulation of SERPINA1E, CFD (adipsin), LIFR. Some of these changes were only significantly reverted using aerobic exercise as a preventative measure, but not as a treatment regime. To determine if either the intensity, or duration, of exercise influenced the outcome, we compared high-intensity interval training (HIIT) and endurance running. Endurance running slightly outperformed HIIT exercise, but overall both provided similar reversion in abundance of plasma proteins modulated by the high-fat diet including SERPINA7, APOE, SERPINA1E, and CFD. Finally, we compared the changes induced by over-consumption of HFD to previous data from mice fed an isocaloric high saturated fat (SFA) or polyunsaturated fat (PUFA) diet. This identified several common changes including increased APOC2 and APOE, but also highlighted changes specific for either over-consumption of HFD (ALDOB, SERPINA7, CFD), SFA-based diets (SERPINA1E), or PUFA-based diets (Haptoglobin - Hp). Together, these data highlight the importance of early intervention with exercise to revert HFD-induced phenotypes and suggest some of the molecular mechanisms leading to the changes in the plasma proteome generated by high fat diet consumption in both mice and humans.
2020-11-02 | PXD018561 | Pride
Project description:Elderly AA volunteers confirmed MCI assigned into a six-month program of aerobic exercise (eleven participants) underwent a 40-minute supervised-training 3-times/week and controls (eight participants) performed stretch training. Participants had maximal oxygen consumption (VO2max) test and Genome-wide methylation levels at CpG sites using the Infinium HumanMethylation450 BeadChip assay at baseline and after a six-month exercise program.
2022-12-31 | E-MTAB-11166 | biostudies-arrayexpress
Project description:Tumor chemoresistance is often associated to high aerobic glycolysis rates and reduced oxidative phosphorylation by cancer cells, a phenomenon called the “Warburg effect”. Thus, a treatment reversing the Warburg effect could decrease tumor cell survival both in the presence or absence of chemotherapy. Short-term starvation (STS) could accomplish this task since it is accompanied by a glucose and amino acid decrease and fatty acid increase, which require respiration for energy production. We tested the cytotoxicity of STS+Oxaliplatin on colon cancer cells by Trypan Blue, Carboxyfluorescein Succinimidyl ester and Annexin V staining. Reactive oxygen species production was measured by 2',7'-dichlorodihydrofluorescein diacetate staining. In vitro glucose consumption was evaluated by 18F-Fluoro-deoxyglucose uptake. Gene expression was tested by microarray analysis. Protein expression and activity were studied by western blot, proteomic analyses and spectrophotometric assays. CT26 bearing mice consumed only water for 48 hours (STS) before oxaliplatin treatment. Dynamic micro-Positron Emission Tomography and tumor growth measurements were performed. STS+Oxaliplatin cause a potent suppression of colon carcinoma growth and glucose consumption in in vitro and in vivo models. In CT26 cells, STS down-regulates aerobic glycolysis, and glutaminolysis, while increasing oxidative phosphorylation. STS-dependent increase in O2 consumption is associated with reduced ATP synthesis and increased oxidation. In combination with chemotherapy, these effects of STS cause additive toxicity to cancer cells. Our findings indicate that during and following STS the decreased glucose levels promote an anti-Warburg effect characterized by increased oxygen consumption but failure to generate ATP, resulting in oxidative damage and apoptosis. The experiment comprised for conditions: Control, Starvation, Oxaliplatin, and Starvation plus Oxaliplatin
2015-08-11 | E-GEOD-60653 | biostudies-arrayexpress
Project description:The synthetic microbial community used in this study was composed of the major functional guilds (cellulolytic fermenter, sulfate reducer, hydrogenotrophic methanogen and acetoclastic methanogen) that mediate the anaerobic conversion of cellulosic biomass to CH4 and CO2 in wetland soils. The choice of a facultative sulfate-reducing bacterium (Desulfovibrio vulgaris Hildenborough) introduced metabolic versatility and enabled investigations into the community response to sulfate intrusion. The growth status of these multi-species cultures was measured over a week by daily analysis of substrate consumption and product accumulation. The quad-cultures were analyzed with metaproteomics at the end of experiment to characterize the community structure and metabolic activities.
2023-02-17 | PXD035759 | Pride
Project description:Sorbose resistant Candida albicans mutant strain [Sor125(55)] derived from parental strain [3153A] has characteristic Ch5 monosomy plus Ch4/7b trisomy. ChIP-chip data showed marked elevation of H4 histone acetylation on monosomic Ch5 in Sor125(55) mutant compared with parental strain (3153A). There was no remarkable diffrence in H4 acetylation level on other chromosomes between those strains and no difference in H3 acetylation on all chromosomes.
2017-10-31 | GSE81684 | GEO