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ABSTRACT:
PROVIDER: PRJNA1212782 | ENA |
REPOSITORIES: ENA
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Project description:Metaproteomics enables the description of microbial communities (MC). Microbial adaptation to changing environments is conducted by expressing newly synthesized proteins (nP) that can be difficult to distinguish from background proteins. Focusing on nP would add a new dimension to the metaproteomics of MC. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising approach to label nP without significantly influencing the natural behavior of MC. However, direct detection of the BONCAT-labeled nP is limited due to their low abundance compared to total protein. Consequently, enrichment of the BONCAT-labeled nP is essential. We present a workflow using click chemistry (CC) and affinity chromatography to isolate nP from MC. The workflow was developed using a mixture of E. coli (labeled) and yeast (unlabeled control) as a test system. The established workflow was also applied to an MC of a laboratory biogas reactor (LBR).
2024-10-17 | PXD047252 | Pride
Project description:DNA methylation profiling of nucleus Accumbens of rats that self administered cocaine, were subjected to 30 withdrawal days, were treated with aCSF, RG108 or SAM and were subjected to extinction tests. The groups consist of: 1. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days, were injected in the nucleus accumbens with aCSF and were subjected to an extinction test for assessment of cue-induced cocaine-seeking behavior (aCSF) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days, were injected in the nucleus accumbens with RG108 and were subjected to an extinction test for assessment of cue-induced cocaine-seeking behavior (RG108) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days, were injected in the nucleus accumbens with SAM and were subjected to an extinction test for assessment of cue-induced cocaine-seeking behavior (SAM)
2015-02-27 | E-GEOD-66347 | biostudies-arrayexpress
Project description:Exoproteomics of Hopland soil isolates. Metabolic trait to efficiently utilize plant polymers provides the energy-expensive microbial adaptation to survive in low carbon availability soil.
2019-07-01 | MSV000084044 | MassIVE
Project description:Gene expression profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests. The groups consist of 1. Saline rats (Sal.) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day (1W) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day and to an extinction test for assessment of cue-induced cocaine-seeking behavior (1C) 4. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days (30W) 5. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days and to an extinction test for assessment of cue-induced cocaine-seeking behavior (30C)
2015-02-27 | E-GEOD-66349 | biostudies-arrayexpress
Project description:DNA methylation profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests. The groups consist of 1. Saline rats (Sal.) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day (1W) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day and to an extinction test for assessment of cue-induced cocaine-seeking behavior (1C) 4. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days (30W) 5. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days and to an extinction test for assessment of cue-induced cocaine-seeking behavior (30C)
2015-02-27 | E-GEOD-66348 | biostudies-arrayexpress
Project description:Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. The repression of pcnB could improve the stability and abundance of the transcripts involved in proton-consuming system, conferring a global improvement on cell membrane, redox state, and energy level. These physiological advantages facilitated further identification of acrD repression enhancing FFAs efflux. The engineered strain pcnBi-acrDi-fadR+ achieved 35.1 g l−1 FFAs production in fed-batch fermentation, which is the maximum titer in E. coli reported to date. This study underscores the significance of hidden genetic determinants in microbial biosynthesis and sheds light on the role of microbial physiologies in boosting microbial biosynthesis.
2024-05-26 | GSE267827 | GEO
Project description:Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. The repression of pcnB could improve the stability and abundance of the transcripts involved in proton-consuming system, conferring a global improvement on cell membrane, redox state, and energy level. These physiological advantages facilitated further identification of acrD repression enhancing FFAs efflux. The engineered strain pcnBi-acrDi-fadR+ achieved 35.1 g l−1 FFAs production in fed-batch fermentation, which is the maximum titer in E. coli reported to date. This study underscores the significance of hidden genetic determinants in microbial biosynthesis and sheds light on the role of microbial physiologies in boosting microbial biosynthesis.
2024-05-21 | GSE267710 | GEO
Project description:Fermenting microbial communities generate hydrogen: its removal through production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction, and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs, and together with mass spectrometry of metabolites, show that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD+/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.
2010-05-22 | GSE21906 | GEO