Ontology highlight
ABSTRACT:
PROVIDER: PRJNA773140 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16547400.fastq.gz | Fastqsanger.gz | |||
| SRR16547401.fastq.gz | Fastqsanger.gz | |||
| SRR16547402.fastq.gz | Fastqsanger.gz | |||
| SRR16547403.fastq.gz | Fastqsanger.gz | |||
| SRR16547404.fastq.gz | Fastqsanger.gz |
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Project description:The use of biofertilizers is becoming an economical and environmentally friendly alternative to promote sustainable agriculture. Biochar from microalgae can be applied to enhance the productivity of food crops through soil improvement, slow nutrient absorption and release, increased water uptake, and long-term mitigation of greenhouse gas sequestration. Therefore, the aim of this study was to evaluate the stimulatory effects of biochar produced from Spirulina platensis biomass on the development and seed production of rice plants. Biochar was produced by slow pyrolysis at 300°C, and characterization was performed through microscopy, chemical, and structural composition analyses. Molecular and physiological analyses were performed in rice plants submitted to different biochar concentrations (0.02, 0.1, and 0.5 mg mL-1) to assess growth and productivity parameters. Morphological and physicochemical characterization revealed a heterogeneous morphology and the presence of K and Mg minerals in the biochar composition. Chemical modification of compounds post-pyrolysis and a highly porous structure with micropores were observed. Rice plants submitted to 0.5 mg mL-1 of biochar presented a decrease in root length, followed by an increase in root dry weight. The same concentration influenced seed production, with an increase of 44% in the number of seeds per plant, 17% in the percentage of full seeds per plant, 12% in the weight of 1,000 full seeds, 53% in the seed weight per plant, and 12% in grain area. Differential proteomic analyses in shoots and roots of rice plants submitted to 0.5 mg mL-1 of biochar for 20 days revealed a fine-tuning of resource allocation towards seed production. These results suggest that biochar derived from Spirulina platensis biomass can stimulate rice seed production.
2024-09-16 | PXD051225 | Pride
Project description:Effects of Biochar Amendments on Soil Microbial Composition
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Project description:Metabolite concentrations can regulate gene expression, which can in turn regulate metabolic activity. The extent to which functionally related transcripts and metabolites show similar patterns of concentration changes, however, remains unestablished. We have therefore measured and analyzed the metabolomic (previously published in Brauer et al., PMID 17159141) and transcriptional responses (presented here) of Saccharomyces cerevisiae to carbon and nitrogen starvation. The transcriptomes of filter cultures of FY4 (a prototrophic, Mata derivative of S288C presented by Winston et al., PMID 7762301) were sampled during exponential growth in minimal media and at 10, 30, 60, 120, 240, and 480 minutes following a switch to media lacking ammonium (nitrogen starvation) or D-glucose (carbon starvation). Transcriptional profiles were measured using an Agilent Yeast Oligo Microarray (V2), with the zero timepoint (i.e. exponential growth) as the reference sample. This yielded 2 time-courses of 6 time-points each. Further information is available in the accompanying manuscript.
2009-02-01 | E-GEOD-11754 | biostudies-arrayexpress
Project description:Microcosm carbon amendments
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Project description:Platelet lysate (PL) demonstrates antimicrobial and anti-inflammatory properties and may offer potential for treatment of bacterial pneumonia in horses. It remains unknown whether nebulization represents a suitable method of administration of PL in horses. This study characterized particle size and flow rate of pooled equine PL nebulized using an equine-specific nebulizer (Flexivent). Protein composition and antimicrobial activity were compared before and after nebulization. Protein composition was evaluated according to growth factor, antimicrobial peptide and cytokine concentrations and proteomic analysis. To evaluate antimicrobial activity, bacterial growth inhibition [maximum growth (µmax); carrying capacity (K)] were determined for E.coli, Streptococcus equi subsp zooepidemicus and Rhodococcus equi (WT and MDR) using pre- and post-nebulized PL concentrations of 50%. Flow rate and median particle size were 0.8 ml/min and 4.991 µm with 52% of particles ≤ 5 µm. Cytokine, growth factor, and antimicrobial peptide concentrations and proteomic profiles were similar pre- and post-nebulization. For all bacteria, nebulization did not alter effect of PL on growth parameters. Negative effects of PL treatments on K were noted for S. zooepidemicus (p= 0.009 all) compared to BHI. No effect of PL was observed on µmax for S.zooepidemicus and on K and µmax for E.coli. For R. equi (WT and MDR), K and µ were positively affected by PL treatments (p≤ 0.05). We concluded that nebulization does not appear to meaningfully impact PL bacterial growth inhibition or protein composition. Further research is recommended to better characterize PL antimicrobial activity against clinically relevant pathogens and suitability for nebulization in horses.
2024-12-26 | PXD055023 | JPOST Repository
Project description:In this study, we investigated the transcriptome of Bifidobacterium bifidum PRL2010 during in vitro growth by micro array technology. When B. bifidum PRL2010 was grown in liquid broth, 425 of the 1644 PRL2010 genes represented on the array were expressed in at least one of the three investigated growth phases, i.e., lag-, exponential and stationary phase. These transcriptional analyses identified a core in vitro transcriptome encompassing 150 genes, which resulted expressed in all phases. A proportion of the latter genes were further investigated as potential reference genes by Quantitative Real Time PCR (qRT-PCR) assays. Their expression stability was evaluated under different growth conditions, encompassing cultivation on different carbon sources, exposure to environmental stresses (thermal, acidic and osmotic) and growth phases. Our analyses validated six reference genes suitable for normalizing mRNA expression levels in qRT-PCR experiments applied to bifidobacteria. Transcriptional profiling of B.bifidum PRL2010 at different growth phases (lag phase, early exponential phase, late exponential phase, early stationary phase).
2012-01-05 | E-GEOD-30832 | biostudies-arrayexpress
Project description:Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. Biphenyl dioxygenase gene (bphA) abundance on four BC types demonstrated corn kernel biochar hosted at least four orders of magnitude more attached cells per gram than other feedstocks, and microscopic imaging revealed the attached live cell fraction was >1.5X more on corn kernel biochar than GAC. BC characteristics (i.e., sorption potential, surface area, pH) drove cell attachment differences. Reverse transcription qPCR indicated BC feedstocks significantly influenced bphA expression in attached cells. The bphA transcript-per-gene ratio of attached cells was >10-fold more than suspended cells, confirmed by transcriptomics. RNA-seq also demonstrated significant upregulation of biphenyl and benzoate degradation pathways on attached cells, revealing biofilm formation potential and cell-cell communication pathway connections. These novel findings demonstrate aerobic PCB-degrading cell abundance and activity could be tuned by adjusting BC feedstocks/ attributes to improve LC-PCBs biodegradation.
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Project description:DZNep (3-deazaneplanocin A) is commonly used to reduce lysine methylation. DZNep inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), preventing the conversion of S-adenosyl-L-homocysteine (SAH) into L-homocysteine and reducing the level of S-adenosylmethionine (SAM). As a result, the SAM to SAH ratio decreases, an indicator of the methylation potential within a cell. Many studies have characterized the impact of DZNep on histone lysine methylation or in specific cell or disease contexts. Recently, protein thermal stability has provided a new dimension for studying the mechanism of action of small molecule inhibitors. In addition to ligand binding, post-translational modifications and protein-protein interactions impact thermal stability. Here, we sought to characterize protein thermal stability changes induced by DZNep treatment in HEK293T cells using the Protein Integral Solubility Alteration (PISA) assay. DZNep treatment altered the thermal stability of 135 proteins, with over half previously reported to be methylated at lysine residues. In addition to thermal stability, we identify changes in transcript and protein abundance after DZNep treatment to distinguish between direct and indirect impacts on thermal stability. Nearly one-third of the proteins with altered thermal stability had no changes at the transcript or protein level. Of these thermally altered proteins, CDK6 had a stabilized methylated peptide, while its unmethylated counterpart was unaltered. Multiple methyltransferases were among the proteins with thermal stability alteration, including DNMT1, potentially due to changes in SAM/SAH levels. This study systematically evaluates DZNep’s impact on the transcriptome, the proteome, and the thermal stability of proteins.
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