Metaproteomics of Daqu Samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Rhizopus Arrhizus Var. Tonkinensis Lichtheimia Ramosa B5399 Aspergillus Oryzae Rib326
SUBMITTER: 
Yan Xu
PROVIDER: PXD059703 | iProX | Sat Jan 11 00:00:00 GMT 2025
REPOSITORIES: iProX
Similar Datasets
Project description:Along with lipidomic and metabolomic analyses, we analysed the effect of short-term heat stress on Nicotiana tabacum pollen tubes. Tubes were either grown for 3 hours at room temperature, for 6 hours at room temperature or for 3 hours at room temperature and then 37 °C for another 3 hours.
2021-06-26 | GSE153474 | GEO
Project description:Metaproteomics is a valuable approach to characterize the biological functions involved in the gut microbiota (GM) response to dietary interventions. Ketogenic diets (KDs) are very effective in controlling seizure severity and frequency in drug-resistant epilepsy (DRE) and in the weight loss management in obese/overweight individuals. This case study provides proof of concept for the suitability of metaproteomics to monitor changes in taxonomic and functional GM features in an individual on a short-term very low-calorie ketogenic diet (VLCKD, 4 weeks), followed by a low-calorie diet (LCD). A marked increase in Akkermansia and Pseudomonadota was observed during VLCKD and reversed after the partial reintroduction of carbohydrates (LCD), in agreement with the results of previous metagenomic studies. In functional terms, the relative increase in Akkermansia was associated with an increased production of proteins involved in response to stress and biosynthesis of gamma-aminobutyric acid. In addition, VLCKD caused a relative increase in enzymes involved in the synthesis of the beta-ketoacid acetoacetate and of the ketogenic amino acid leucine. Our data support the potential of fecal metaproteomics to investigate the GM-dependent effect of KD as a therapeutic option in obese/overweight individuals and DRE patients.
2024-12-23 | PXD055204 | Pride
Project description:The aim of this study was to develop a suitable method to preserve fecal samples for metaproteomics analyses when flash-freezing is not an option. Fecal samples were collected from conventional adult C57BL/6 mice and combined into a fecal master mix. The fecal master mix was then split into 48 subsamples that were subjected to different preservation treatments. The following six preservation methods were tested: flash-freezing in liquid nitrogen followed by storage at -80°C, immersion in RNAlater® and storage at room temperature, immersion in RNAlater® and immediate storage at -80°C, immersion in 95% ethanol and storage at room temperature, immersion in a RNAlater-like buffer “NAP buffer” and storage at room temperature, and immersion in an autoclaved RNAlater-like buffer “Autoclaved NAP buffer” and storage at room temperature. Proteins were extracted from the samples after being stored for 1 and 4 weeks. There were 4 replicates per treatment and time-point. Samples were analyzed by LC-MS/MS and the data were analyzed with Proteome Discoverer against a large database of mouse microbiota protein sequences.
2021-11-25 | PXD024115 | Pride
Project description:Background and aims: In Crohn’s disease (CD) patients on combination therapy (infliximab and immunosuppressant) and stopping infliximab (STORI cohort), the risk of short-term (<6 months) and mid/long-term relapse (>6 months) was associated with specific blood protein profiles. Our aim was to test the external validity of this finding in the SPARE cohort.
Methods: The SPARE trial included patients with CD in sustained steroid-free clinical remission, on combination therapy and randomly allocated to one of three arms: continuing combination therapy, stopping infliximab or stopping immunosuppressant. As it was performed in STORI, 202 immune-related proteins were measured in the baseline serum of SPARE (arm stopping infliximab, n=63-67). The proteins associated with time to relapse (univariable Cox model) were compared between STORI and SPARE. The external validation of biomarkers (individually and combined by pairs) was evaluated by a discrimination analysis (c-statistic) and compared to CRP, faecal calprotectin and a previously validated model (CEASE).
Results: In STORI and SPARE, specific blood protein profiles were associated with the risk of short-term (eg, high level: CRP, HP, IL6, CLEC4C, 3.5<HR<17.5, p<0.05) and mid/long-term relapse (eg, low level: FLT3LG, SERPINA4, FGF2, 0.15<HR<0.36, p<0.05). At external validation, our top 10 biomarker pairs showed a higher discriminative ability (c-statistic) than the CEASE model, CRP and faecal calprotectin to predict short-term (0.76-0.80 vs 0.74 vs 0.71 vs 0.69, respectively ) and mid/long-term relapse (0.66-0.68 vs 0.61 vs 0.52 vs 0.59, respectively).
Conclusion: In CD patients stopping infliximab, we confirm that the risk of short-term and mid/long-term relapse is associated with specific blood protein profiles showing the potential to guide infliximab withdrawal.
2024-08-31 | PXD051233 | panorama
Project description:Aims: To obtain small non-coding RNA expression profiles of short-term activated and long-term activated hepatic stellate cells (HSCs). To obtain small non-coding RNA expression profiles of small extracellular vesicles (sEVs) from short-term activated and long-term activated HSCs. Methods: Primary rat HSCs were isolated and cultured in vitro. To isolate HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Day 3 HSCs, Day 14 HSCs, and HSC-sEVs were collected and lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.
2024-08-29 | E-MTAB-12764 | biostudies-arrayexpress
Project description:In order to study in detail short and mid term heat stress molecular response we performed a shotgun proteomics study. One-year-old P. radiata seedlings (plant size ∼33 ± 4 cm) were kept in 1 dm3 pots under a photoperiod of 16 h (400 µmol m−2 s−1) at 25 °C and 50% relative humidity (RH), and 15 °C and 60% RH during the night period. The plants were previously acclimated over a 1-month period inside the climate chamber, being watered with nutritive solution (N : P : K, 5 : 8 : 10). In order to perform a realistic experiment, and corresponding with the dawn, heat exposure treatment began with an increasing temperature gradient from 15 to 40 °C over 5 h, which was then maintained for 6 h; after that, temperature was gradually decreased from 40 to 15 °C over 5 h. This experimental procedure was repeated for 5 days and sampling was performed at: 3 h after 40 °C was reached on Day 1 (T1/2) and at the end of the 6 h heat exposure on Day 1 (T1), Day 2 (T2), Day 3 (T3) and Day 5 (T5) (Figure 1a). Plants were watered every day to 80% full capacity (FC) in order to avoid a collateral drought stress. A group of control plants was also collected on Day 1 (C) before starting the heat exposure.
2023-03-11 | PXD032754 | Pride
Project description:Frozen dough baking is useful method in the modern bread-making industry. However, the fermentation activity of bakerâs yeast dramatically decreased after thawing due to freeze injuries, because bakerâs yeast cells contained in dough experience freeze injuries during freeze-thaw processes. Here, we performed genome-wide expression analysis to determine genetic response in bakerâs yeasts under freeze-thaw condition using a DNA microarray analysis. Functional and clustering analyses in gene expression reveal that genes could be characterized by the term of freeze-thaw stress. Under short-term freeze stress (freeze treatment for 3 day), genes involved in ribosomal protein were up-regulated. Under long-term freeze stress (freeze treatment for longer than 7 day), genes involved in energy synthesis were up-regulated. In each phase, genes involved in protein damage, several stresses and trehalose and glycogen metabolism were also up-regulated. Through these freeze stress, yeast cells may improve reduced efficiency of translation and enhanced cell protection mechanism to survive under freeze stress condition. These regulations of these genes would be controlled by the cAMP-protein kinase A pathway. Experiment Overall Design: All experiments were done in duplicate from two independent samples.
2009-08-09 | E-GEOD-8673 | biostudies-arrayexpress
Project description:Frozen dough baking is useful method in the modern bread-making industry. However, the fermentation activity of baker’s yeast dramatically decreased after thawing due to freeze injuries, because baker’s yeast cells contained in dough experience freeze injuries during freeze-thaw processes. Here, we performed genome-wide expression analysis to determine genetic response in baker’s yeasts under freeze-thaw condition using a DNA microarray analysis. Functional and clustering analyses in gene expression reveal that genes could be characterized by the term of freeze-thaw stress. Under short-term freeze stress (freeze treatment for 3 day), genes involved in ribosomal protein were up-regulated. Under long-term freeze stress (freeze treatment for longer than 7 day), genes involved in energy synthesis were up-regulated. In each phase, genes involved in protein damage, several stresses and trehalose and glycogen metabolism were also up-regulated. Through these freeze stress, yeast cells may improve reduced efficiency of translation and enhanced cell protection mechanism to survive under freeze stress condition. These regulations of these genes would be controlled by the cAMP-protein kinase A pathway. Keywords: baker’s yeast, freeze-thaw stress, gene expression, freezing period
2009-07-31 | GSE8673 | GEO
Project description:The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
2022-06-07 | GSE178279 | GEO