iSO1949_N.oceanica, Genome-scale metabolic model of Nannochloropsis oceanica

S. van Oossanen; N. Ferrer Ledo; V.A.P. Martins dos Santos; M.J. Barbosa; M. Suarez Diez; S. D'Adamo

doi:10.5281/zenodo.10658526

iSO1949_N.oceanica, Genome-scale metabolic model of Nannochloropsis oceanica

S. van Oossanen, N. Ferrer Ledo (Other), V.A.P. Martins dos Santos (Other), M.J. Barbosa (Other), M. Suarez Diez (Other), S. D'Adamo (Other)

Research output: Non-textual form › Software

Abstract

Genome-scale constraint-based metabolic model (GEM) of the oleaginous microalga Nannochloropsis oceanica. Build through orthology-based reconstruction with AuReMe, using the scaffold GEMs iCre1355 (Chlamyomonas reinhardtii), iLB1027_lipid (Phaeodactylum tricornutum), iRJ1321 (Microchloropsis gaditana) and iNS934 (Microchloropsis salina). Specifically curated on the lipid metabolism of N. oceanica. Contains two 'light acclimation modes', based on continuous steady state cultures acclimated to low light and high light. We used the biomass compositions and oxygen-based photosynthesis-irradiance (PI) curves to set the biomass equation and the non-growth associated maintenance rates. The GEM can predict the effect of light acclimation on CO2-based PI-curves.

Developed by the Bioprocess Engineering (BPE) department and the laboratory of Systems and Synthetic Biology (SSB) of the Wageningen University and Research. Additional information available upon request.

Original language	English
Publisher	Wageningen University & Research
DOIs	https://doi.org/10.5281/zenodo.10658526
Publication status	Published - 14 Feb 2024

Access to Document

10.5281/zenodo.10658526Licence: CC BY

Cite this

@misc{223bdab55ea3464fa4d6bd6f31e2a758,

title = "iSO1949_N.oceanica, Genome-scale metabolic model of Nannochloropsis oceanica",

abstract = "Genome-scale constraint-based metabolic model (GEM) of the oleaginous microalga Nannochloropsis oceanica. Build through orthology-based reconstruction with AuReMe, using the scaffold GEMs iCre1355 (Chlamyomonas reinhardtii), iLB1027_lipid (Phaeodactylum tricornutum), iRJ1321 (Microchloropsis gaditana) and iNS934 (Microchloropsis salina). Specifically curated on the lipid metabolism of N. oceanica. Contains two 'light acclimation modes', based on continuous steady state cultures acclimated to low light and high light. We used the biomass compositions and oxygen-based photosynthesis-irradiance (PI) curves to set the biomass equation and the non-growth associated maintenance rates. The GEM can predict the effect of light acclimation on CO2-based PI-curves.Developed by the Bioprocess Engineering (BPE) department and the laboratory of Systems and Synthetic Biology (SSB) of the Wageningen University and Research. Additional information available upon request.",

author = "{van Oossanen}, S. and {Ferrer Ledo}, N. and {Martins dos Santos}, V.A.P. and M.J. Barbosa and {Suarez Diez}, M. and S. D'Adamo",

year = "2024",

month = feb,

day = "14",

doi = "10.5281/zenodo.10658526",

language = "English",

publisher = "Wageningen University & Research",

address = "Netherlands",

}

TY - ADVS

T1 - iSO1949_N.oceanica, Genome-scale metabolic model of Nannochloropsis oceanica

AU - van Oossanen, S.

A2 - Ferrer Ledo, N.

A2 - Martins dos Santos, V.A.P.

A2 - Barbosa, M.J.

A2 - Suarez Diez, M.

A2 - D'Adamo, S.

PY - 2024/2/14

Y1 - 2024/2/14

N2 - Genome-scale constraint-based metabolic model (GEM) of the oleaginous microalga Nannochloropsis oceanica. Build through orthology-based reconstruction with AuReMe, using the scaffold GEMs iCre1355 (Chlamyomonas reinhardtii), iLB1027_lipid (Phaeodactylum tricornutum), iRJ1321 (Microchloropsis gaditana) and iNS934 (Microchloropsis salina). Specifically curated on the lipid metabolism of N. oceanica. Contains two 'light acclimation modes', based on continuous steady state cultures acclimated to low light and high light. We used the biomass compositions and oxygen-based photosynthesis-irradiance (PI) curves to set the biomass equation and the non-growth associated maintenance rates. The GEM can predict the effect of light acclimation on CO2-based PI-curves.Developed by the Bioprocess Engineering (BPE) department and the laboratory of Systems and Synthetic Biology (SSB) of the Wageningen University and Research. Additional information available upon request.

AB - Genome-scale constraint-based metabolic model (GEM) of the oleaginous microalga Nannochloropsis oceanica. Build through orthology-based reconstruction with AuReMe, using the scaffold GEMs iCre1355 (Chlamyomonas reinhardtii), iLB1027_lipid (Phaeodactylum tricornutum), iRJ1321 (Microchloropsis gaditana) and iNS934 (Microchloropsis salina). Specifically curated on the lipid metabolism of N. oceanica. Contains two 'light acclimation modes', based on continuous steady state cultures acclimated to low light and high light. We used the biomass compositions and oxygen-based photosynthesis-irradiance (PI) curves to set the biomass equation and the non-growth associated maintenance rates. The GEM can predict the effect of light acclimation on CO2-based PI-curves.Developed by the Bioprocess Engineering (BPE) department and the laboratory of Systems and Synthetic Biology (SSB) of the Wageningen University and Research. Additional information available upon request.

U2 - 10.5281/zenodo.10658526

DO - 10.5281/zenodo.10658526

M3 - Software

PB - Wageningen University & Research

ER -

iSO1949_N.oceanica, Genome-scale metabolic model of Nannochloropsis oceanica

Abstract

Access to Document

Fingerprint

Cite this