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: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.
Project description:The aim was to characterize epigenetic changes in histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings using mass spectrometry-based approach. Increased level of histone H3.3 variant was found to be the most prominent feature of 20-day-old calli, associated with chromatin relaxation. Methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate and trichostatin A, although each HDACi affected the state of post-translational histone modifications in a specific manner.
