Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1222586 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32315869_1.fastq.gz | Fastqsanger.gz | |||
| SRR32315869_2.fastq.gz | Fastqsanger.gz | |||
| SRR32315870_1.fastq.gz | Fastqsanger.gz | |||
| SRR32315870_2.fastq.gz | Fastqsanger.gz | |||
| SRR32315871_1.fastq.gz | Fastqsanger.gz |
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Project description:Polylactic acid (PLA) is a promising biodegradable material used in various fields, such as mulching films and disposable packaging materials. Biological approaches for completely degrading biodegradable polymers can provide environmentally friendly solutions. However, to our knowledge, no studies have performed transcriptome profiling to analyze PLA-degrading genes of PLA-degrading bacteria. Therefore, this study reports for the first time an RNA sequence approach for tracing genes involved in PLA biodegradation in the PLA-degrading bacterium Brevibacillus brevis. In the interpretation results of the differentially expressed genes, the hydrolase genes mhqD and nap and the serine protease gene besA were up-regulated by a fold change of 7.97, 4.89, and 4.09, respectively. This result suggests that hydrolases play a key role in PLA biodegradation by B. brevis. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes implicated in biofilm formation were upregulated. The biodegradation of PLA starts with bacteria attaching to the surface of PLA and forming a biofilm. Therefore, it could be confirmed that the above genes were up-regulated for access to PLA and biodegradation. Our results provide transcriptome-based insights into PLA biodegradation, which pitch a better understanding of microbial biodegradation of plastics.
2025-01-16 | GSE223668 | GEO
Project description:Compost Used for PLA Degradation Raw sequence reads
| PRJNA979101 | ENA
Project description:Biodegradable plastics, such as polylactic acid (PLA), are widely considered as sustainable alternatives to fossil fuel-derived polymers; however, their degradation generates polylactic acid microplastics (PLA-MPs), which raises ecological concerns in freshwater ecosystems. In this study, we investigated the responses of Microcystis aeruginosa to PLA-MPs (1, 10, and 50 mg/L) across a 45-day co-culture experiment. We found the PLA-MPs initially inhibited algal growth (days 18, 27) through oxidative stress, as indicated by elevated MDA content (1.94 nmol/mg protein at 50 mg/L, 1.57 times higher than the control) and SOD activity (1.30 U/mg Protein, 2.45 times higher than the control). However, during stabilization (days 36 and 45), PLA-MPs promoted growth in a dose-dependent manner, with Chl-a content in the 1, 10, and 50 mg/L groups reaching 1.12, 1.36, and 1.44 times that of the control, respectively. Concurrent shifts in inorganic carbon speciation, EPS secretion, and cellular aggregation highlighted dynamic adaptation strategies. Finally, based on the proteomic analysis, it was found that PLA-MPs promoted the growth of M. aeruginosa by improving photosynthetic efficiency, enhancing the expression of the TCA cycle and oxidative phosphorylation, and promoting cell division and proliferation. Our results confirm that PLA-MPs have a long-term effect on the growth of M. aeruginosa, providing fundamental theoretical guidance for investigating the ecological and environmental impacts of PLA-MPs in aquatic ecosystems.
| PXD069473 |
Project description:Context: Yanghe Pingchuan decoction (YPD) has been used for asthma treatment for many years in China. Objective: We sought to understand the role of YPD, and find more potential targets for YPD-based treatment of asthma. Materials and methods: An ovalbumin-induced asthma model in rats was created. Staining (hematoxylin and eosin, Masson) was used to evaluate the treatment effect of YPD. RNA-sequencing was carried out to analyze global gene expression, and differentially expressed genes (DEGs) were identified. Analysis of the functional enrichment of genes was done using the Gene Ontology database. Analysis of signaling-pathway enrichment of genes was done using the Kyoto Encyclopedia of Genes and Genomes database. Real-time reverse transcription-quantitative polymerase chain reaction was undertaken to measure expression of DEGs. Results: Pathology showed that YPD had an improvement effect on rats with asthma. RNA-sequencing showed that YPD led to upregulated and downregulated expression of many genes. The YPD-based control of asthma pathogenesis may be related to calcium ion (Ca2+) binding, inorganic cation transmembrane transporter activity, microtubule motor activity, and control of canonical signaling (e.g., peroxisome proliferator-activated receptor, calcium, cyclic adenosine monophosphate). Enrichment analyses suggested that asthma pathogenesis may be related to Ca2+ binding and contraction of vascular smooth muscle. A validation experiment showed that YPD could reduce the Ca2+ concentration by inhibiting the Ang-Ⅱ/PLA/CaM signaling axis. Discussion and conclusion: Control of asthma pathogenesis by YPD may be related to inhibition of the Ang-Ⅱ/PLA/CaM signaling axis, reduction of the Ca2+ concentration, and relaxation of airway smooth muscle.
2023-11-07 | GSE247032 | GEO
Project description:The obese, insulin resistant state is characterized by impairments in lipid metabolism. Dietary polyphenols might improve these deteriorations. We have previously shown that 3-days supplementation of combined Epigallocatechin-gallate and Resveratrol (E+R) increased energy expenditure, which was accompanied by improved metabolic flexibility after a high-fat mixed-meal (HFMM) in men. The present study aimed to investigate whether these short-term effects translate into longer-term improvement of insulin sensitivity and lipid metabolism. In this randomized, double-blind study, 42 overweight subjects (21 male, 38±2 yrs, BMI 29.7±0.5 kg/m2, HOMA-IR 2.1±0.2) received either E+R (300 and 80 mg/d, respectively) or placebo (PLA) for 12 weeks (3 months). Before (t0) and after (t3) intervention, tissue-specific insulin sensitivity was assessed by a hyperinsulinemic-euglycemic clamp with stable isotope infusion. Fasting and postprandial (HFMM) lipid metabolism was assessed using indirect calorimetry and blood sampling. Adipose tissue and skeletal muscle lipolysis was measured using microdialysis in men and skeletal muscle biopsies were collected to assess mitochondrial function and gene expression alterations via microarray analysis. E+R supplementation increased fasting (P=0.06) and postprandial (P=0.03) fat oxidation but did not alter energy expenditure compared to PLA. This was accompanied by an E+R-induced increase in oxidative capacity in permeabilized muscle fibers (p<0.05). Moreover, E+R supplementation attenuated the increase in plasma triacylglycerol concentration that was observed in the PLA group (AUC, p<0.05), and tended to decrease visceral fat mass (P=0.09). Finally, insulin-stimulated glucose disposal and suppression of endogenous glucose production were not affected by E+R supplementation. 12 weeks E+R supplementation increased whole-body fat oxidation and skeletal muscle oxidative capacity, but this did not translate into increased tissue-specific insulin sensitivity in overweight and obese subjects. To identify pathways that may underlie the E+R-induced improvement of skeletal muscle mitochondrial capacity, we performed microarray analysis on skeletal muscle biopsies (vastus lateralis muscle), collected before and after 12-weeks E+R or PLA treatment. Gene Set Enrichment Analysis (GSEA) indicated that the most upregulated pathways after E+R supplementation were related to the citric acid cycle and respiratory electron transport chain, while pathways related to carbohydrate metabolism were upregulated in the PLA group. In this randomized, double-blind placebo-controlled, parallel intervention trial, subjects received either a combination of E+R supplements (INTV, 282 mg/d and 80 mg/d, respectively) or placebo (PLA, partly hydrolyzed microcrystalline cellulose-filled capsules) for a period of 12 weeks (3 months) to assess effects of E+R supplementation on tissue-specific insulin sensitivity (primary outcomes) and fasting and postprandial substrate metabolism (secondary outcomes). Skeletal muscle (m. vastus lateralis) biopsies were taken under local anesthesia during fasting conditions before (t0) and after the 12-weeks (t3) intervention period. Extraxted RNA was hybridized on HTA 2.0 Affymetrix arrays and microarray analysis was performed on paired sample sets for 27 subjects (p, PLA n = 14; E+R n = 13).
2016-08-03 | E-GEOD-71614 | biostudies-arrayexpress
Project description:<p>The phycosphere is an important ecological niche for bacteria and antibiotic resistance genes (ARGs). However, whether and how the interaction between microalgae and bacteria changed, and its further effect on the transmission of ARGs under pollutant stress remains enigmatic. Here, Auxenochlorella pyrenoidosa was co-cultured with bacteria screened from lake water to explore the algal-bacteria interaction and ARGs transmission in the presence of florfenicol (FF) and polylactic acid microplastics (PLA MPs). Our study demonstrated that the growth and metabolism of A. pyrenoidosa were promoted under FF treatment or co-treatment with PLA MPs, validated by phenotypic, transcriptome, and metabolome analyses. In contrast, the abundance of phycospheric bacteria was decreased as a result of niche competition. Nonetheless, the transmission of ARGs in the phycosphere was promoted due to the enrichment of antibiotic-resistant bacteria, especially Pseudomonas, rather than horizontal gene transfer. Algal-bacteria co-culture experiment further suggested that vitamin B6 secreted by Pseudomonas sp. likely contributes to underpinning A. pyrenoidosa survival under FF and PLA MPs stress. These findings underscore the dynamic interplay and co-evolution between algae and bacteria under pollutant exposure, and reveal a potential mechanism of vitamin B6-mediated mutualism. This study provides new insights into the assembly of phycospheric bacterial communities and the adaptive strategies of microalgae in contaminated aquatic environments.</p>
2025-09-26 | MTBLS11371 | MetaboLights