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Created: 12th Dec 2022 at 13:41
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Projects: SilicoTryp, Multiscale modelling of state transitions in the host-microbiome-brain network, MESI-STRAT, PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University of Groningen

I am a Professor in Medical Systems Biology and the University Medical Centre Groningen. The research in my lab is focused on complex regulation of mammalian lipid and carbohydrate metabolism, eventually aiming at network-based therapies. We combine dynamic computer simulations with quantitative metabolomics, 13C fluxomics, proteomics and transcriptome analysis, and in depth biochemical analysis. This allows to predict and understand ‘emergent’ properties, those properties that are counterintuitive ...
Projects: PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University of Leiden
Projects: PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University Medical Centre Groningen
PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.
Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease ...
Programme: This Project is not associated with a Programme
Public web page: http://polimer-itn.eu/
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Models
Snapshots: No snapshots
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: ACAD activity partitioning, HepG2 oxygen consumption, Whole-body ketogenic flux
Snapshots: No snapshots
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Comparing acyl-CoA dehydrogenase deficiencies, MCADD patient personalised modelling, MCADD rescue titration
Snapshots: No snapshots
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model construction
Organisms: No organisms
Models: Model notebooks, Text S1. Model description, odendaal1, odendaal2, odendaal3
SOPs: Parameter Search SOP
Data files: No Data files
Snapshots: No snapshots
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"
Submitter: Christoff Odendaal
Biological problem addressed: Validation
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model validation
Organisms: Homo sapiens (batch)
Models: Model notebooks, odendaal2
SOPs: No SOPs
Data files: HepG2 protein concentration for O2 consumption ..., Oxygen concentration and consumption flux in pe...
Snapshots: No snapshots
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"
Submitter: Christoff Odendaal
Biological problem addressed: Validation
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model validation
Organisms: No organisms
Models: Model notebooks, odendaal1
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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".
Submitter: Christoff Odendaal
Biological problem addressed: Validation
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model validation
Organisms: No organisms
Models: Model notebooks, odendaal3
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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, ...
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model analysis
Organisms: No organisms
Models: Model notebooks, odendaal1
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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" ...
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model analysis
Organisms: No organisms
Models: Model notebooks, odendaal1
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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".
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model analysis
Organisms: No organisms
Models: Model notebooks, odendaal1
SOPs: No SOPs
Data files: Table S4. Fibroblasts proteomics
Snapshots: No snapshots
Flux and CoASH concentration control coefficients of odendaal1 at cytosolic [palmitoyl-CoA] = 10 and 150 µM.
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model analysis
Assays: 1 hidden item
Symptomatic and asymptomatic MCADD individuals' urine acylcarnitines under metabolic decompensation, after an overnight fast, and after feeding, respectively. The source of Table 1 from the associated article.
Creators: Christoff Odendaal, Emmalie Jager, Terry G.J. Derks, Barbara Bakker, Rebecca Heiner-Fokkema
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model analysis
Assays: 1 hidden item
Proteomics from MCADD and control individuals' fibroblasts.
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks, Karin Wolters; Anne-Claire Martines
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model analysis
Measured in an Oroboros oxygraph.
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna, Albert Gerding; Nicolette Huijkman; Marcel Vieira-Lara; Anne-Claire Martines
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model validation
Assays: HepG2 oxygen consumption
Protein measurement used to normalised the oxygen consumption flux measured on an Oroboros oxygraph.
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna, Albert Gerding; Nicolette Huijkman; Marcel Vieira-Lara; Anne-Claire Martines
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model validation
Assays: HepG2 oxygen consumption
Creators: Christoff Odendaal, Emmalie Jager, Terry G.J. Derks, Barbara Bakker
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
Organism: Homo sapiens
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Models
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.
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Homo sapiens
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model analysis, Model construction, Model validation
Assays: ACAD activity partitioning, Comparing acyl-CoA dehydrogenase deficiencies, HepG2 oxygen consumption, MCADD patient personalised modelling, MCADD rescue titration, Models, Whole-body ketogenic flux and 2 hidden items
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).
Creators: Christoff Odendaal, Emmalie Jager, Terry G.J. Derks, Barbara Bakker
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Homo sapiens
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction, Model validation
Assays: HepG2 oxygen consumption, Models
Human mitochondrial fatty acid oxidation of saturated, even chain acyl-Coas beginning at C16. See Model description for detail.
Creators: Christoff Odendaal, Emmalie Jager, Barbara Bakker, Terry G.J. Derks
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model analysis, Model construction, Model validation
Assays: Comparing acyl-CoA dehydrogenase deficiencies, MCADD patient personalised modelling, MCADD rescue titration, Models, Whole-body ketogenic flux and 2 hidden items
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).
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Homo sapiens
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction, Model validation
Assays: ACAD activity partitioning, Models
Creators: Christoff Odendaal, Barbara Bakker
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Models
Abstract (Expand)
Authors: Christoff Odendaal, Emmalie Jager, Anne-Claire M. F. Martines, Marcel A. Vieira-Lara, Nicolette C. A. Huijkman, Ligia Akemi Kiyuna, Albert Gerding, Justina C. Wolters, Rebecca Heiner-Fokkema, Karen van Eunen, Terry G.J. Derks, Barbara Bakker
Date Published: No date defined
Publication Type: Journal
Citation:
Patient characteristics pertaining to fibroblasts used for modle personalisation.
Creators: Christoff Odendaal, Emmalie Jager, Terry G.J. Derks, Barbara Bakker, Anne-Claire Martines; Karin Wolters
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model analysis
Reasoning underlying the conversion made ot compare the model to validation data. Supplementary Text S2 in the associated article.
Creators: Christoff Odendaal, Emmalie Jager, Barbara Bakker, Terry G.J. Derks
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model validation
Assays: ACAD activity partitioning, HepG2 oxygen consumption, Whole-body ketogenic flux