ABSTRACT: Untargeted metabolomics of Botrytis-Bacillus interaction at 6,24 and 48h. Ethyl-acetate extraction of supernatant fraction and methanol extraction for cell fraction.
Project description:Transcriptome sequencing of mice treated with Chebulae Fructus hydrosoluble extract ethyl acetate fraction and water were performed, and the gene expression profiles were compared.
Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper. B subtilis NCIB3610 cells were grown in the presence of Aspergillus niger CB 119.1 hyphae for 3 hours. The mycelium and the attached bacteria were separated from the non-attached B. subtilis cells via filtration through Miracloth. The mycelia and attached bacteria were briefly rinsed with TY medium, dried, and the sample was frozen in liquid nitrogen. Bacterial cells in the flow-through medium fraction were harvested by centrifugation at 10.397 g for 1 min. To extract RNA mainly from the bacterial cells, lysozyme solution and RiboLock (Thermo Scientific) was added followed by incubation at 37 C for 30 minutes. Further RNA extraction was performed with the Macaloid/Roche method as described before (van Hijum et al., 2005, Kovács and Kuipers, 2011) but omitting the bead beater treatment and using RiboLock.
Project description:The fungus Pycnoporus coccineus was grown either alone or in presence of another fungus (here: Coniophora puteana or Botrytis cinerea) in order to study the fungal interspecific interaction mechanisms.
Project description:Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper.
Project description:The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, the single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for a 10 ng, 250ng and 10µg peptide sample, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the robust approach even for simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.
Project description:LC-MS/MS Non-targeted metabolomics of fungi-bacteria co-cultures for antagonism study. Bacterial, fungi and interaction agar samples were taken to do the ethyl acetate metabolites extraction
Project description:The associated files are mass spec data from mixed-bed ion exchange chromatogrphy fractions. Starting extract was 14,000 x g clarified supernatant from extraction of liquid nitrogen powdered Chenopodium quinoa seeds. Extraction buffer was 20 mM HEPES pH 7.6, 130 mM K-acetate, 5 mM Mg-acetate, 0.1 mM EDTA, 10% glycerol, 1 mM DTT, phosphatase inhibitors, and Plant specific protease inhibitors.