Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1122190 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR29443878_1.fastq.gz | Fastqsanger.gz | |||
| SRR29443878_2.fastq.gz | Fastqsanger.gz | |||
| SRR29443879_1.fastq.gz | Fastqsanger.gz | |||
| SRR29443879_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
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Project description:Abnormal circadian rhythms, including exposure to light at night, are associated with a higher cancer risk and a poorer prognosis, which may be one of the reasons that the incidence of cancer is increasing in individuals subjected to these stresses. However, the molecular or systemic mechanisms involved in tumor growth under artificial illumination stress conditions have not been identified. In fact, the question of whether artificial illumination stress promotes tumor growth at all is still controversial. To identify the possible mechanisms underlying tumor progression related to circadian rhythms, we set up nude mouse xenograft models. Eight-week-old male nude mice (BALBc nu/nu) were injected with 100ul (1x106 cells) of Hela cells suspension at two separate dorsal sites. Mice were randomly caged (5/cage) and subdivided into L/L (24-hour light cycle; circadian rhythm disruption model) and L/D (12-hour light/dark cycle; normal circadian rhythm model) groups. 11days after injection, we sacrificed one L/L mouse and one L/D mouse, tumors were immediately preserved using liquid nitrogen. Total RNA from tumors were isolated using QIAshredder and RNeasy-Mini kits (Qiagen).
2011-09-12 | GSE23969 | GEO
Project description:Anaerobic ammonium oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome predictions. Here, we experimentally resolved the central carbon metabolism using metabolomics (LC-MS and GC-MS), metabolic flux analysis and proteomics (shot-gun proteomics).
2021-07-30 | PXD016171 | Pride
Project description:Abnormal circadian rhythms, including exposure to light at night, are associated with a higher cancer risk and a poorer prognosis, which may be one of the reasons that the incidence of cancer is increasing in individuals subjected to these stresses. However, the molecular or systemic mechanisms involved in tumor growth under artificial illumination stress conditions have not been identified. In fact, the question of whether artificial illumination stress promotes tumor growth at all is still controversial. To identify the possible mechanisms underlying tumor progression related to circadian rhythms, we set up nude mouse xenograft models. Eight-week-old male nude mice (BALBc nu/nu) were injected with 100ul (1x106 cells) of Hela cells suspension at two separate dorsal sites. Mice were randomly caged (5/cage) and subdivided into L/L (24-hour light cycle; circadian rhythm disruption model) and L/D (12-hour light/dark cycle; normal circadian rhythm model) groups. 11days after injection, we sacrificed one L/L mouse and one L/D mouse, tumors were immediately preserved using liquid nitrogen. Total RNA from tumors were isolated using QIAshredder and RNeasy-Mini kits (Qiagen). We compared the transcriptional profiling of L/L tumor which was derived from 24-hour light cycle (L/L) caging mice with the transcriptional profiling of L/D tumor which was derived from 12-hour light/dark cycle (L/D) caging mice.
2011-09-11 | E-GEOD-23969 | biostudies-arrayexpress
Project description:Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.
2022-03-01 | GSE147041 | GEO
Project description:<p _msttexthash='40138319' _msthash='17867'>Background Ammonia-oxidizing bacteria (AOB) play a crucial role in the microbiome of the global nitrogen cycle. Yet, their regulatory functions in the metabolic pathways involved in organic material stabilization (OMS) are not fully understood. We employed metabolomics, microbiomics, and molecular biology techniques to investigate for the first time the metabolic changes and regulatory mechanisms of OMS in a cow manure and straw biostabilization system inoculated with a novel exogenous consortium-AOB (C-AOB). </p><p _msttexthash='40138319' _msthash='17867'>Results C-AOB engaged in nitrogen metabolism during the thermophilic phase and participated in carbon metabolism during the stabilization phase of OMS. Glutamate was a key metabolite bridging the carbon and nitrogen metabolic networks, which increased during humic formation. C-AOB inoculation stimulated NO2- production, enhanced glycolysis and the tricarboxylic acid cycle, thereby facilitating glutamate conversion and contributing to humic formation. Additionally, NO2- served as a nitrogen source for microbial proliferation, thus enhancing microbial community activity and stability. The observed increase in the abundance of amoA, that encodes ammonia monooxygenase, indicates a close association between C-AOB inoculation and increased glutamate content. </p><p _msttexthash='40138319' _msthash='17867'>Conclusions The key metabolites, enzymes, and genes, particularly those associated with glutamate, played a role in regulating OMS by C-AOB. These findings underscore the regulatory roles of AOB in the metabolic pathways involved in OMS, which is of global concern.</p>
2025-10-23 | MTBLS13207 | MetaboLights
Project description:Resendis-Antonio2007 - Genome-scale metabolic
network of Rhizobium etli (iOR363)
This model is described in the article:
Metabolic reconstruction and
modeling of nitrogen fixation in Rhizobium etli.
Resendis-Antonio O, Reed JL,
Encarnación S, Collado-Vides J, Palsson BØ.
PLoS Comput. Biol. 2007 Oct; 3(10):
1887-1895
Abstract:
Rhizobiaceas are bacteria that fix nitrogen during symbiosis
with plants. This symbiotic relationship is crucial for the
nitrogen cycle, and understanding symbiotic mechanisms is a
scientific challenge with direct applications in agronomy and
plant development. Rhizobium etli is a bacteria which provides
legumes with ammonia (among other chemical compounds), thereby
stimulating plant growth. A genome-scale approach, integrating
the biochemical information available for R. etli, constitutes
an important step toward understanding the symbiotic
relationship and its possible improvement. In this work we
present a genome-scale metabolic reconstruction (iOR363) for R.
etli CFN42, which includes 387 metabolic and transport
reactions across 26 metabolic pathways. This model was used to
analyze the physiological capabilities of R. etli during stages
of nitrogen fixation. To study the physiological capacities in
silico, an objective function was formulated to simulate
symbiotic nitrogen fixation. Flux balance analysis (FBA) was
performed, and the predicted active metabolic pathways agreed
qualitatively with experimental observations. In addition,
predictions for the effects of gene deletions during nitrogen
fixation in Rhizobia in silico also agreed with reported
experimental data. Overall, we present some evidence supporting
that FBA of the reconstructed metabolic network for R. etli
provides results that are in agreement with physiological
observations. Thus, as for other organisms, the reconstructed
genome-scale metabolic network provides an important framework
which allows us to compare model predictions with experimental
measurements and eventually generate hypotheses on ways to
improve nitrogen fixation.
This model is hosted on
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MODEL1507180006.
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2015-07-30 | MODEL1507180006 | BioModels
Project description:Purpose: To compare RNASeq data of Frankia strains (EAN1pec, EuIC and EUN1f) under nitrogen stress. Frankia cultures were grown for 2 days under nitrogen replete (+NH4) or nitrogen- deficient (N2) conditions. RNA-seq analysis provided insight into how the the bacteria responds to nitrogen stress.
2018-04-18 | GSE64517 | GEO