Christoff Odendaal

Validation of model's ability to predict oxygen consumption flux as measured usign permeabilised cells in an Oroboros Oxygraph. Generates Fig. 2A in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "4, Fig2A-Oroboros-simulation-data-[needs-(1-2-and-3)]-20221109.nb" after running "1, generate-model-20221109.nb"

Validation of model's ability to predict whole-body ketogeneic flux as extracted form Fletcher et al. (2019). Generates Fig. 2B in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "5, Fig2B-ketogenesis-validation-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Testing the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Generates Fig. 2 C and D in the associated publication. Data from Aoyama et al. (1995).

Downoad and unzip "Model_notebooks.rar" and run "6, Fig2C+D-ACAD-partitioning-validation-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb".

Minireviews about each enzyme in the mitochindrial beta-oxidation model on which the final parameter choices (fixed-parameter model) and parameter sampling distributions (ensemble) were based.

Prediction of patient urinary acylcarnitine under metabolic decompensation. Generates Fig. 3, Table 1, and Table S2 in the associated publication.

Download and unzip "Model_notebooks.rar" and run "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Based on odendaal1, a control model is made and compared to model deficient for short-chain acyl-CoA dehydrogenase (SCADD, 0%), medium-chain acyl-CoA dehydrogenase (MCADD, 0%), and very long-chain acyl-CoA dehydrogenase (VLCADD, 10%). With and withou metabolite partitioning, and with a fixed mitohondrial free CoASH. Generates Figures 3, 4, S1, S2, and S3 in the related paper.

Download "Model_notebooks.rar", unzip, and run: "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" and "14, ...

Calculation of control and response coefficients. Generates Fig. 5, Fig. S4, and Table S2 in the associated publication.

Download "Model_notebooks.rar", unzip, and run: "8, Fig5-control-coefficients-[needs-(1)]-20221109.nb", "9, TableS2-response-coefficients-[needs-(1)]-20230302.nb", and "15, FigS4-control-coefficients-low-AcetylCoA-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"

Incrementally increase the activity of some target rescue enzymes from 20% of default expression to 200% of default expression in a control and MCADD model to see if flux and CoASH concentration are rescued. Generates Fig. 6, S5, and S6.

Download "Model_notebooks.rar", unzip, and run "11, Fig6+S5-rescues-[needs-(1-and-10)]-20221109.nb", "10, Fig6B-inset-rescues-(low-acetylCoA)-[needs-(1)]-20221109.nb", and "16, FigS6-rescues-20221109-fixed-[needs-(1)]-CoASH.nb" after running "1, generate-model-20221109.nb" ...

Creation of personalised models of control, symptomatic MCADD, asymptomatic MCADD, and early diagnosis MCADD individuals using fibroblast proteomics to adjust model Vmaxes. Generates Fig. 7 and S7.

Download and unzip "Model_notebooks.rar" and run "13, Fig7-personalised-models-[needs-(1-and-12)]-20221109.nb" after running "1, generate-model-20221109.nb" and "12, Fig7-S7-preprocessing-[needs-(1)-]-20221109.nb".

Protein measurement used to normalised the oxygen consumption flux measured on an Oroboros oxygraph.

Measured in an Oroboros oxygraph.

Proteomics from MCADD and control individuals' fibroblasts.

Adjusted model to test the model's ability to oxygen consumption rate by permeabilised HepG2 cells in an Oroboros oxygraph. Data from Fletcher et al. (2019).

Adjusted model to test the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Data from Aoyama et al. (1995).

Human mitochondrial fatty acid oxidation of saturated, even chain acyl-Coas beginning at C16. See Model description for detail.

Unzip model notebooks and keep in the same folder. Notebook names state which notebooks need to be run before them in order for them to word, e.g. "[needs-(1)]" indicates that the notebook numbered 1 must be run and its exported output generated before the given notebook can work. This has to do with the model being generated in only one notebook to avoid duplication.

Medium-/short-chain hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)

Medium-chain ketoacyl-CoA thiolase (EC 2.3.1.16)

Mitochondrial trifunctional protein (UniProt: P40939)

Acyl-CoA thioesterases (EC 3.1.2.1. and EC 3.1.2.2)

L-carnitine as conserved moiety

CoA as conserved moiety

Acetyl-CoA in the mitochondrion as constant metabolite

NADH and NAD+ (Nicotinamide adinine dinucleotide) as constant values.

Oxidised and reduced electron transferring flavoprotein as constant values.

Volume per mg mitochondrial protein of mitochondrion and cytosol.

Carnitine palmitoyltransferase 1 (EC 2.3.1.21)

The theory, calculations, and conditions that went into estimating the Keqs.

Carnitine acylcarnitine translocase (UniProt: O43772)

Carnitine palmitoyltransferase 2 (EC 2.3.1.21)

Carnitine acetyltransferase (EC 2.3.1.7)

Short-chain acyl-CoA dehydrogenase (EC 1.3.99.2)

Medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3)

Very long-chain acyl-CoA dehydrogenase (EC 1.3.8.9)

Crotonase / Enoyl-CoA hydratase (EC 4.2.1.17)

A short description of the experiments conducted to decide on HepG2 cells as the appropriate line for the generation of an MCAD knockout. IHH, Hep3B, HepG2, and HUH-7 cells were all consdered.