Project description:Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 µM Pb(NO3)2.
Project description:The project intended to reveal protein phosphorylation patterns in Arabidopsis thaliana in response to ATP. For this purpose, Arabidopsis thaliana plants, including WT, ATP receptor mutants (p2k1, p2k2, and double mutant p2k1/p2k2), and P2K1 overexpression plants, were treated with ATP or buffer (as the negative control). Crude membrane proteins were then extracted, reduced with DTT, alkylated with iodoacetamide, and digested with Lys-C/trypsin. The digested peptides were then acidified with formic acid, desalted with C18 SPE columns, and concentrated in a Speed-Vac concentrator. The Phosphopeptides were enriched from the above digested peptide samples using IMAC and then analyzed with LC-MS/MS. Data was searched with MaxQuant (ver. 2.0.1.0), which identified and quantified peptides and proteins across all of with Arabidopsis thaliana data set (Uniprot.2020.11.02).
Project description:In this study we explain the physiological, biochemical and gene expression mechanisms adopted by ammonium nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses A transcriptomic analysis enabled the identification of photoassimilate allocation and remobilization as fundamental process used by the plants to maintain the outstanding photosynthetic performance. Moreover, based on the relationship between plant carbon status and hormone functioning, the transcriptomic analyses provided an explanation of why phenology accelerates in elevated [CO2] conditions.
Project description:In this study we explain the physiological, biochemical and gene expression mechanisms adopted by ammonium nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses A transcriptomic analysis enabled the identification of photoassimilate allocation and remobilization as fundamental process used by the plants to maintain the outstanding photosynthetic performance. Moreover, based on the relationship between plant carbon status and hormone functioning, the transcriptomic analyses provided an explanation of why phenology accelerates in elevated [CO2] conditions.
Project description:The goal of this study is to compare the transcriptome (RNA-seq) modulations in the roots and shoots of Arabidopsis thaliana, as a plant model, exposed to two toxic concentrations of rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively.
Project description:A major limitation in quantitative time-course proteomics is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity, high dynamic samples such as plant extracts, this is tradeoff is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Field Asymetric Waveform Ion Mobility Spectrometry (FAIMSpro) settings using the latest label-free, single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply-quantify the Arabidopsis thaliana seedling proteome at microliter per minute flow rates. Using a micro-flow BoxCar DIA acquisition workflow with -30, -50, -70 CV FAIMSpro settings we are able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-minute gradient, facilitating the analysis of ~48 samples per day. Utilizing this acquisition approach, we next performed an abiotic stress time-course experiment, whereby we quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress. Here, we successfully quantify over >6400 shoot and >8500 root protein groups, respectively, quantifying nearly 9700 unique protein groups total across the study. Collectively, we pioneer a fast-flow, multi-CV FAIMSpro BoxCar DIA acquisition workflow that represents an exciting new analysis approach for quantitative time-course proteomics experimentation in plants.
