SEEK ID: https://fairdomhub.org/people/1369
Location:
Netherlands
ORCID:
https://orcid.org/0000-0002-9872-2102
Joined: 26th May 2019
Expertise: Not specified
Tools: Not specified
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- Projects (1)
- Institutions (1)
- Investigations (0+2)
- Studies (1+2)
- Assays (5+5)
- Data files (2)
- Models (1)
- Publications (2)
- Presentations (0+8)
- Documents (8+1)
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
Following on in silico and in vitro work, the effect of MCAD deficiency on CoA metabolism was investigated. Using a recently published HILIC-MS/MS method, free and acylated CoA species could be measured simultaneously in HepG2 MCAD-KO cells. The levels of CoA biosynthesis intermediates and total CoA was also characterised by HPLC in liver samples from MCAD-KO mice exposed to energetic stress (fasting adn cold). qPCR was applied to investigate changes in the CoA metabolism that might constitute ...
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Computational model (in silico), HepG2 cells (in vitro), Mice (in vivo)
Snapshots: Snapshot 1
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
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
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.
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model construction
Organisms: No organisms
Models: No Models
SOPs: Parameter Search SOP
Data files: No Data files
Snapshots: Snapshot 1
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Organisms: No organisms
Models: Model notebooks, odendaal4
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
The behaviour of a published MCAD-KO HepG2 cell line was compared to that of a wild-type HepG2 cell line in terms of the changes in acyl-CoA and acylcarnitine levels (measured by HILIC-MS/MS) and gene expression pertaining to CoA metabolism (characterised by qPCR). Additionally, the incorporation of label from stable isotope-labelled pantothenate (vitamine B5) was over 24 hours of exposure to an energetic stressor was also investigated.
Submitter: Christoff Odendaal
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Organisms: Homo sapiens (batch)
SOPs: No SOPs
Data files: HepG2 CoA labelling data, palmitate/no-glucose ..., HepG2 acyl-CoA measurements, palmitate/low-gluc..., HepG2 acyl-CoA measurements, palmitate/no-gluco..., HepG2 acyl-CoA/acylcarnitine measurements stati..., HepG2 acyl-CoA/acylcarnitine measurements stati..., HepG2 acylcarnitine measurements, palmitate/low..., HepG2 acylcarnitine measurements, palmitate/no-..., HepG2 qPCR statistical significance, palmitate/..., HepG2 qPCR statistical significance, palmitate/..., HepG2 qPCR, palmitate/low-glucose (Fig. S11), HepG2 qPCR, palmitate/no-glucose (Fig. S9)
Snapshots: No snapshots
MCAD-KO mice (C57BL/6J background) were exposed to three different conditions: "fed", "fasting", and "fasting + cold". In this study we determined the concentration of various CoA biosynthetic intermediates (including CoA) and the expression of CoA metabolic genes in liver tissue samples from these groups of mice.
Submitter: Christoff Odendaal
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Organisms: No organisms
SOPs: No SOPs
Data files: Mice CoA biosynthetic intermediates (Fig. 4C), Mice qPCR (Fig. 4E-F)
Snapshots: No snapshots
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
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
Creators: Christoff Odendaal, Ligia Akemi Kiyuna, Madhulika Singh, Barbara Bakker, Amy HARMS, Thomas Hankemeier
Submitter: Christoff Odendaal
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Sequestration of CoA and adaptation of CoA meta...
Assays: Computational model (in silico)
Abstract (Expand)
Authors: Madhulika Singh, Ligia Akemi Kiyuna, Christoff Odendaal, Barbara M. Bakker, Amy C Harms, Thomas Hankemeier
Date Published: 11th Sep 2023
Publication Type: Journal
DOI: 10.26434/chemrxiv-2023-h0w52
Citation: [Preprint]
Abstract (Expand)
Authors: C. Odendaal, E. A. Jager, A. M. F. Martines, M. A. Vieira-Lara, N. C. A. Huijkman, L. A. Kiyuna, A. Gerding, J. C. Wolters, R. Heiner-Fokkema, K. van Eunen, T. G. J. Derks, B. M. Bakker
Date Published: 4th Sep 2023
Publication Type: Journal
PubMed ID: 37667308
Citation: BMC Biol. 2023 Sep 4;21(1):184. doi: 10.1186/s12915-023-01652-9.
L-carnitine as conserved moiety
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
CoA as conserved moiety
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
Acetyl-CoA in the mitochondrion as constant metabolite
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
NADH and NAD+ (Nicotinamide adinine dinucleotide) as constant values.
Creators: Christoff Odendaal, Ligia Akemi Kiyuna, Barbara Bakker
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
Oxidised and reduced electron transferring flavoprotein as constant values.
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
Volume per mg mitochondrial protein of mitochondrion and cytosol.
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
Medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3)
Creators: Christoff Odendaal, Barbara Bakker, Ligia Akemi Kiyuna
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model construction
Assays: Kinetics Minireviews
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.
Creators: Christoff Odendaal, Barbara Bakker, Terry G.J. Derks, Ligia Akemi Kiyuna, Emmalie Jager
Submitter: Christoff Odendaal
Investigations: Mitochondrial fatty acid oxidation in human liver
Studies: Model validation
Assays: HepG2 oxygen consumption