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Neiburga2022 - Arabidopsis thaliana MEP pathway with cis-abienol synthesis

ABSTRACT: 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

SUBMITTER: Reinis Muiznieks

PROVIDER: MODEL2206090002 | BioModels | 2023-02-04

REPOSITORIES: BioModels

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Neiburga2022 - Arabidopsis thaliana MEP pathway with isoprene synthesis

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

2023-02-04 | MODEL2206090003 | BioModels

Neiburga2022 - Arabidopsis thaliana wild-type MEP pathway kinetic model

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2023-02-04 | MODEL2206090001 | BioModels

Berzins2022 - Crypthecodinium cohnii: ethanol uptake for production of DHA precursor acetyl-CoA

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2022-05-06 | MODEL2112290001 | BioModels

Berzins2022 - Crypthecodinium cohnii: glucose and glycerol uptake for production of DHA precursor acetyl-CoA

Project description:This model is a supplementary material of publication “Kinetic and stoichiometric modeling-based analysis of do-cosahexaenoic acid (DHA) production potential by C.cohnii from glycerol, glucose and ethanol” by Kristaps Berzins, Reinis Muiznieks, Matiss R. Baumanis, Inese Strazdina, Karlis Shvirksts, Santa Prikule, Vytautas Galvanauskas, Daniel Pleissner, Agris Pentjuss, Mara Grube, Uldis Kalnenieks and Egils Stalidzans This is a kinetic model of Crypthecodinium cohnii central carbon metabolism during fatty acid synthesis. The model is aimed at cytosolic acetyl coenzyme-A production, which is the precursor of fatty acids. The model contains 35 reactions and 36 species split into three compartments – extracellular, cytosol and mitochondria. It was assumed that dry weight accounts for 33% of wet weight and that 1ml = 1g. The mitochondria volume is 1% of cytosol volume. Both glucose and glycerol can be used as substrates in this model, however, the model was designed for single substrate use only. For use of ethanol as substrate, see MODEL2112290001 . The model is preset for steady state calculation using glucose. To use glycerol as a substrate it is possible to change species concentrations manually or use the predefined parameter set. The model contains 31 global quantities which were used to optimize the model during parameter estimation. These global quantities include amino acid concentrations for each enzyme, the total amino acid concentration used in enzymes, the sum transport reaction variable parameters and the total concentration of species. All enzymatic reactions contain a parameter k, which can be used for change of enzyme expression levels in case of optimization of product flux or yield. Currently all the parameters k are set for 1, which corresponds to wild-type. The model was made for steady-state. For glucose and glycerol a steady state resolution of 1e-6 can be used.

2022-05-06 | MODEL2112280001 | BioModels

Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

Project description:Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation.

2012-05-31 | GSE29687 | GEO

Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

2012-05-31 | E-GEOD-29687 | biostudies-arrayexpress

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Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with cis-cinnamic acid.

2012-07-01 | GSE37862 | GEO

Arabidopsis thaliana: cis-cinnamic acid-treated seedlings versus control seedlings

Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with cis-cinnamic acid. Two-condition experiment, cis-cinnamic acid-treated seedlings vs. control seedlings. Biological replicates: 2 control replicates, 2 cis-cinnamic acid treated.

2012-06-30 | E-GEOD-37862 | biostudies-arrayexpress

Arabidopsis thaliana:seedlings treated by cis-cinnamic acid derivatives versus control seedlings

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2013-12-28 | GSE51400 | GEO

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