Project description:Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. To study the role of autophagy during submergence, we performed transcriptome analysis with atg5, an autophagy-defective mutant, under submergence conditions. Our data showed that submergence changed the expression profile of DEG in the atg5 versus wild-type.
Project description:It is the study to investigate the growth and transcriptome of Arabidopsis thaliana exposed to submergence or flooding with physical flow.
Project description:Kinetic model of extended MEP pathway in Arabidopsis thaliana for isoprene.
This model was used for determining total optimization potential (TOP) of isoprene production in Arabidopsis thaliana using Spacescanner (https://github.com/atiselsts/spacescanner). This model was used to make designs D, E and F. An optimization task in COPASI can be perfomed using this model by accesing COPASI/Tasks/Optimization. Parameters which will be changed during the optimization and the optimization constraints can be selected.
More description in
Total optimization potential (TOP) approach based constrained design of isoprene and cis-abienol production in A. thaliana,
Authors: Katrina D. Neiburga, Reinis Muiznieks, Darta M. Zake, Agris Pentjuss, Vitalijs Komasilovs, Johann Rohwer, Alain Tissier, Egils Stalidzans
Project description:This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level.
Project description:Kinetic model of extended MEP pathway in Arabidopsis thaliana for cis-abienol production.
This model was used for determining total optimization potential (TOP) of cis-abienol production in Arabidopsis thaliana using Spacescanner (https://github.com/atiselsts/spacescanner). This model was used to make designs A, B and C. An optimization task in COPASI can be perfomed using this model by accesing COPASI/Tasks/Optimization. Parameters which will be changed during the optimization and the optimization constraints can be selected.
More description in
Total optimization potential (TOP) approach based constrained design of isoprene and cis-abienol production in A. thaliana,
Authors: Katrina D. Neiburga, Reinis Muiznieks, Darta M. Zake, Agris Pentjuss, Vitalijs Komasilovs, Johann Rohwer, Alain Tissier, Egils Stalidzans
