Project description:Cesium (Cs) is known to exert toxicity in plants by competition and interference with the transport of potassium (K). However, the precise mechanism of how Cs mediates its damaging effect is still unclear. To identify putative genes that are functionally involved in this response, RNA-seq was conducted on Arabidopsis roots grown in low K and Cs medium conditions. Comparison of both stress condition reveals Cs alters ABA signaling during seed germination and induced expression of thiamine biosnynthesis genes.
Project description:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.
Project description:Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.
Project description:Deep sequencing of the 5' ends of uncapped, polyA-enriched mRNA from two biological replicate samples from Arabidopsis thaliana inflorescences, as well as two biological replicates of Arabidopsis lyrata inflorescences. These data were used to experimentally identify sliced microRNA targets from the two species.
Project description:Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in ribosomal RNAs of all three sub-cellular transcriptomes in Arabidopsis thaliana. m5C sites in rRNAs were also anlyzed in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5, NOP2A, NOP2B and NOP2C.
