Kava (Piper methysticum) is an ethnomedicinal shrub native to the Polynesian islands with well-established anxiolytic and analgesic properties. Its main psychoactive principles, kavalactones, form a unique class of polyketides that interact with the human central nervous system through mechanisms distinct from those of conventional psychiatric drugs. However, an unknown biosynthetic machinery and difficulty in chemical synthesis hinder the therapeutic use of kavalactones. In addition, kava also ...[more]
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:Comparison of expression differences between Col-0 Arabidopsis thaliana and transgenic plants in the same background carrying three different Fusarium oxysporum effector genes Overall design: 4 biological replicates of the wildtype Col-0, 4 biological replicates of the 2 independent Avr2 lines, 3 biological replicates of the 2 independent Six6 lines, 4 biological replicates of the single Six8 line were run on microarrays, leaf material was used to isolate RNA
Project description:deOliveiraDalMolin2010 - Genome-scale
metabolic network of Arabidopsis thaliana (AraGEM)
This model is described in the article:
AraGEM, a genome-scale
reconstruction of the primary metabolic network in
de Oliveira Dal'Molin CG, Quek LE,
Palfreyman RW, Brumbley SM, Nielsen LK.
Plant Physiol. 2010 Feb; 152(2):
Genome-scale metabolic network models have been successfully
used to describe metabolism in a variety of microbial organisms
as well as specific mammalian cell types and organelles. This
systems-based framework enables the exploration of global
phenotypic effects of gene knockouts, gene insertion, and
up-regulation of gene expression. We have developed a
genome-scale metabolic network model (AraGEM) covering primary
metabolism for a compartmentalized plant cell based on the
Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a
comprehensive literature-based, genome-scale metabolic
reconstruction that accounts for the functions of 1,419 unique
open reading frames, 1,748 metabolites, 5,253 gene-enzyme
reaction-association entries, and 1,567 unique reactions
compartmentalized into the cytoplasm, mitochondrion, plastid,
peroxisome, and vacuole. The curation process identified 75
essential reactions with respective enzyme associations not
assigned to any particular gene in the Kyoto Encyclopedia of
Genes and Genomes or AraCyc. With the addition of these
reactions, AraGEM describes a functional primary metabolism of
Arabidopsis. The reconstructed network was transformed into an
in silico metabolic flux model of plant metabolism and
validated through the simulation of plant metabolic functions
inferred from the literature. Using efficient resource
utilization as the optimality criterion, AraGEM predicted the
classical photorespiratory cycle as well as known key
differences between redox metabolism in photosynthetic and
nonphotosynthetic plant cells. AraGEM is a viable framework for
in silico functional analysis and can be used to derive new,
nontrivial hypotheses for exploring plant metabolism.
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Project description:Comparative transcriptomic analysis of Arabidopsis thaliana lines expressing a constitutively active YDA protein (CA-YDA; in La-0 background), and wild-type plants (La-0) non-infected or infected with the necrotrophic fungal pathogen Plectosphaerella cucumerina BMM (PcBMM) Overall design: Gene expression was measured in 18-days old Arabidopsis thaliana plants expressing a constitutively active YDA protein (CA-YDA) and in wild-type plants (La-0) at 1 day after inoculation (1 dpi) with P. cucumerina BMM (PcBMM) or after treatment with water (non-infected or mock treatment). Three independent experiments were performed.
Project description:This SuperSeries is composed of the following subset Series: GSE24571: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata [RNA-Seq] GSE38109: Natural variation in Arabidopsis thaliana transcriptomes Refer to individual Series
Project description:For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary. We employed a trivalent gene expression profiling approach in order to elucidate the changes in gene expression that occur during the early steps of light-induced chloroplast biogenesis. Overall design: The three conditions compared were: Arabidopsis thaliana wildtype Col-0 grown in dark for 4 days after germination. Arabidopsis thaliana mutant pap7 and wildtype col-0 for 5 days in light. Plants were grown separately on MS medium in Petri dish per condition. around 50 seedlings per petridish.