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631 results on '"Bakker, Barbara M"'

10. Rebalancing of mitochondrial homeostasis through an NAD+-SIRT1 pathway preserves intestinal barrier function in severe malnutrition

Author

Ling, Catriona, Versloot, Christian J., Arvidsson Kvissberg, Matilda E., Hu, Guanlan, Swain, Nathan, Horcas-Nieto, José M., Miraglia, Emily, Thind, Mehakpreet K., Farooqui, Amber, Gerding, Albert, van Eunen, Karen, Koster, Mirjam H., Kloosterhuis, Niels J., Chi, Lijun, ChenMi, YueYing, Langelaar-Makkinje, Miriam, Bourdon, Celine, Swann, Jonathan, Smit, Marieke, de Bruin, Alain, Youssef, Sameh A., Feenstra, Marjon, van Dijk, Theo H., Thedieck, Kathrin, Jonker, Johan W., Kim, Peter K., Bakker, Barbara M., and Bandsma, Robert H.J.

Published
2023
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17. Longitudinal Metabolomics Data Analysis Informed by Mechanistic Models.

Author

Li, Lu, Hoefsloot, Huub, Bakker, Barbara M., Horner, David, Rasmussen, Morten A., Smilde, Age K., and Acar, Evrim

Subjects
BODY mass index, TIME-resolved measurements, METABOLIC models, DATA analysis, METABOLOMICS
Abstract

Background: Metabolomics measurements are noisy, often characterized by a small sample size and missing entries. While data-driven methods have shown promise in terms of analyzing metabolomics data, e.g., revealing biomarkers of various phenotypes, metabolomics data analysis can significantly benefit from incorporating prior information about metabolic mechanisms. This paper introduces a novel data analysis approach to incorporate mechanistic models in metabolomics data analysis. Methods: We arranged time-resolved metabolomics measurements of plasma samples collected during a meal challenge test from the COPSAC2000 cohort as a third-order tensor: subjects by metabolites by time samples. Simulated challenge test data generated using a human whole-body metabolic model were also arranged as a third-order tensor: virtual subjects by metabolites by time samples. Real and simulated data sets were coupled in the metabolites mode and jointly analyzed using coupled tensor factorizations to reveal the underlying patterns. Results: Our experiments demonstrated that the joint analysis of simulated and real data had better performance in terms of pattern discovery, achieving higher correlations with a BMI (body mass index)-related phenotype compared to the analysis of only real data in males, while in females, the performance was comparable. We also demonstrated the advantages of such a joint analysis approach in the presence of incomplete measurements and its limitations in the presence of wrong prior information. Conclusions: The joint analysis of real measurements and simulated data (generated using a mechanistic model) through coupled tensor factorizations guides real data analysis with prior information encapsulated in mechanistic models and reveals interpretable patterns. [ABSTRACT FROM AUTHOR]

Published
2025
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23. Analyzing postprandial metabolomics data using multiway models:a simulation study

Author

Li, Lu, Yan, Shi, Bakker, Barbara M., Hoefsloot, Huub, Chawes, Bo, Horner, David, Rasmussen, Morten A., Smilde, Age K., Acar, Evrim, Li, Lu, Yan, Shi, Bakker, Barbara M., Hoefsloot, Huub, Chawes, Bo, Horner, David, Rasmussen, Morten A., Smilde, Age K., and Acar, Evrim

Abstract

Background: Analysis of time-resolved postprandial metabolomics data can improve the understanding of metabolic mechanisms, potentially revealing biomarkers for early diagnosis of metabolic diseases and advancing precision nutrition and medicine. Postprandial metabolomics measurements at several time points from multiple subjects can be arranged as a subjects by metabolites by time points array. Traditional analysis methods are limited in terms of revealing subject groups, related metabolites, and temporal patterns simultaneously from such three-way data. Results: We introduce an unsupervised multiway analysis approach based on the CANDECOMP/PARAFAC (CP) model for improved analysis of postprandial metabolomics data guided by a simulation study. Because of the lack of ground truth in real data, we generate simulated data using a comprehensive human metabolic model. This allows us to assess the performance of CP models in terms of revealing subject groups and underlying metabolic processes. We study three analysis approaches: analysis of fasting-state data using principal component analysis, T0-corrected data (i.e., data corrected by subtracting fasting-state data) using a CP model and full-dynamic (i.e., full postprandial) data using CP. Through extensive simulations, we demonstrate that CP models capture meaningful and stable patterns from simulated meal challenge data, revealing underlying mechanisms and differences between diseased versus healthy groups. Conclusions: Our experiments show that it is crucial to analyze both fasting-state and T0-corrected data for understanding metabolic differences among subject groups. Depending on the nature of the subject group structure, the best group separation may be achieved by CP models of T0-corrected or full-dynamic data. This study introduces an improved analysis approach for postprandial metabolomics data while also shedding light on the debate about correcting baseline values in longitudinal data analysis.

Published
2024

24. Targeted Proteomics to Study Mitochondrial Biology

Author

Wolters, Justina C., Permentier, Hjalmar P., Bakker, Barbara M., Bischoff, Rainer, Cohen, Irun R., Editorial Board Member, Lajtha, Abel, Editorial Board Member, Lambris, John D., Editorial Board Member, Paoletti, Rodolfo, Editorial Board Member, Rezaei, Nima, Editorial Board Member, Urbani, Andrea, editor, and Babu, Mohan, editor

Published
2019
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25. Model-order reduction of biochemical reaction networks

Author

Rao, Shodhan, van der Schaft, Arjan, van Eunen, Karen, Bakker, Barbara M., and Jayawardhana, Bayu

Subjects
Computer Science - Systems and Control, Computer Science - Software Engineering, Mathematics - Dynamical Systems, Physics - Chemical Physics, Quantitative Biology - Molecular Networks
Abstract

In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron reduction of the weighted Laplacian matrix which describes the graph structure of complexes in the chemical reaction network. We apply our method to a yeast glycolysis model, where the simulation result shows that the transient behaviour of a number of key metabolites of the reduced-order model is in good agreement with those of the full-order model., Comment: 7 pages, 5 figures. arXiv admin note: substantial text overlap with arXiv:1211.6643, arXiv:1110.6078

Published
2012

37. Malnutrition-associated liver steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction

Author

van Zutphen, Tim, Ciapaite, Jolita, Bloks, Vincent W., Ackereley, Cameron, Gerding, Albert, Jurdzinski, Angelika, de Moraes, Roberta Allgayer, Zhang, Ling, Wolters, Justina C., Bischoff, Rainer, Wanders, Ronald J., Houten, Sander M., Bronte-Tinkew, Dana, Shatseva, Tatiana, Lewis, Gary F., Groen, Albert K., Reijngoud, Dirk-Jan, Bakker, Barbara M., Jonker, Johan W., Kim, Peter K., and Bandsma, Robert H.J.

Published
2016
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38. Handling Biological Complexity Using Kron Reduction

Author

Jayawardhana, Bayu, Rao, Shodhan, Sikkema, Ward, Bakker, Barbara M., Allgöwer, Frank, Series editor, Morari, Manfred, Series editor, Camlibel, M. Kanat, editor, Julius, A. Agung, editor, Pasumarthy, Ramkrishna, editor, and Scherpen, Jacquelien M.A., editor

Published
2015
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42. Age and Diet Modulate the Insulin-Sensitizing Effects of Exercise: A Tracer-Based Oral Glucose Tolerance Test

Author

Vieira-Lara, Marcel A., Reijne, Aaffien C., Koshian, Serj, Ciapaite, Jolita, Abegaz, Fentaw, Talarovicova, Alzbeta, van Dijk, Theo H., Versloot, Christian J., Bandsma, Robert H.J., Wolters, Justina C., Groen, Albert K., Reijngoud, Dirk Jan, van Dijk, Gertjan, Bakker, Barbara M., Vieira-Lara, Marcel A., Reijne, Aaffien C., Koshian, Serj, Ciapaite, Jolita, Abegaz, Fentaw, Talarovicova, Alzbeta, van Dijk, Theo H., Versloot, Christian J., Bandsma, Robert H.J., Wolters, Justina C., Groen, Albert K., Reijngoud, Dirk Jan, van Dijk, Gertjan, and Bakker, Barbara M.

Published
2023
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43. Hyperglycaemia, pregnancy outcomes and maternal metabolic disease risk during pregnancy and lactation in a lean gestational diabetes mouse model

Author

Tol, Angela J C, Hribar, Kaja, Kruit, Janine, Bongiovanni, Laura, Vieira-Lara, Marcel A, Koster, Mirjam H, Kloosterhuis, Niels J, Havinga, Rick, Koehorst, Martijn, de Bruin, Alain, Bakker, Barbara M, Oosterveer, Maaike H, van der Beek, Eline M, Tol, Angela J C, Hribar, Kaja, Kruit, Janine, Bongiovanni, Laura, Vieira-Lara, Marcel A, Koster, Mirjam H, Kloosterhuis, Niels J, Havinga, Rick, Koehorst, Martijn, de Bruin, Alain, Bakker, Barbara M, Oosterveer, Maaike H, and van der Beek, Eline M

Abstract

Abstract: Hyperglycaemia in pregnancy (HIP) is a pregnancy complication characterized by mild to moderate hyperglycaemia that negatively impacts short- and long-term health of mother and child. However, relationships between severity and timing of pregnancy hyperglycaemia and postpartum outcomes have not been systemically investigated. We investigated the impact of hyperglycaemia developing during pregnancy (gestational diabetes mellitus, GDM) or already present pre-mating (pre-gestational diabetes mellitus, PDM) on maternal health and pregnancy outcomes. GDM and PDM were induced in C57BL/6NTac mice by combined 60% high fat diet (HF) and low dose streptozotocin (STZ). Animals were screened for PDM prior to mating, and all underwent an oral glucose tolerance test on gestational day (GD)15. Tissues were collected at GD18 or at postnatal day (PN)15. Among HFSTZ-treated dams, 34% developed PDM and 66% developed GDM, characterized by impaired glucose-induced insulin release and inadequate suppression of endogenous glucose production. No increased adiposity or overt insulin resistance was observed. Furthermore, markers of non-alcoholic fatty liver disease (NAFLD) were significantly increased in PDM at GD18 and were positively correlated with basal glucose levels at GD18 in GDM dams. By PN15, NAFLD markers were also increased in GDM dams. Only PDM affected pregnancy outcomes such as litter size. Our findings indicate that GDM and PDM, resulting in disturbances of maternal glucose homeostasis, increase the risk of postpartum NAFLD development, related to the onset and severity of pregnancy hyperglycaemia. These findings signal a need for earlier monitoring of maternal glycaemia and more rigorous follow-up of maternal health after GDM and PDM pregnancy in humans. (Figure presented.). Key points: We studied the impact of high-fat diet/streptozotocin induced hyperglycaemia in pregnancy in mice and found that this impaired glucose tolerance and insulin release. Litter size a

Published
2023

44. Rebalancing of mitochondrial homeostasis through an NAD+-SIRT1 pathway preserves intestinal barrier function in severe malnutrition.

Author

Dep Biomolecular Health Sciences, Pathobiologie, Cell Biology, Metabolism & Cancer - Cancer, Ling, Catriona, Versloot, Christian J, Arvidsson Kvissberg, Matilda E, Hu, Guanlan, Swain, Nathan, Horcas-Nieto, José M, Miraglia, Emily, Thind, Mehakpreet K, Farooqui, Amber, Gerding, Albert, van Eunen, Karen, Koster, Mirjam H, Kloosterhuis, Niels J, Chi, Lijun, ChenMi, YueYing, Langelaar-Makkinje, Miriam, Bourdon, Celine, Swann, Jonathan, Smit, Marieke, de Bruin, Alain, Youssef, Sameh A, Feenstra, Marjon, van Dijk, Theo H, Thedieck, Kathrin, Jonker, Johan W, Kim, Peter K, Bakker, Barbara M, Bandsma, Robert H J, Dep Biomolecular Health Sciences, Pathobiologie, Cell Biology, Metabolism & Cancer - Cancer, Ling, Catriona, Versloot, Christian J, Arvidsson Kvissberg, Matilda E, Hu, Guanlan, Swain, Nathan, Horcas-Nieto, José M, Miraglia, Emily, Thind, Mehakpreet K, Farooqui, Amber, Gerding, Albert, van Eunen, Karen, Koster, Mirjam H, Kloosterhuis, Niels J, Chi, Lijun, ChenMi, YueYing, Langelaar-Makkinje, Miriam, Bourdon, Celine, Swann, Jonathan, Smit, Marieke, de Bruin, Alain, Youssef, Sameh A, Feenstra, Marjon, van Dijk, Theo H, Thedieck, Kathrin, Jonker, Johan W, Kim, Peter K, Bakker, Barbara M, and Bandsma, Robert H J

Published
2023

45. Hyperglycaemia, pregnancy outcomes and maternal metabolic disease risk during pregnancy and lactation in a lean gestational diabetes mouse model

Author

Pathobiologie, Dep Biomolecular Health Sciences, Cell Biology, Metabolism & Cancer - Cancer, Tol, Angela J C, Hribar, Kaja, Kruit, Janine, Bongiovanni, Laura, Vieira-Lara, Marcel A, Koster, Mirjam H, Kloosterhuis, Niels J, Havinga, Rick, Koehorst, Martijn, de Bruin, Alain, Bakker, Barbara M, Oosterveer, Maaike H, van der Beek, Eline M, Pathobiologie, Dep Biomolecular Health Sciences, Cell Biology, Metabolism & Cancer - Cancer, Tol, Angela J C, Hribar, Kaja, Kruit, Janine, Bongiovanni, Laura, Vieira-Lara, Marcel A, Koster, Mirjam H, Kloosterhuis, Niels J, Havinga, Rick, Koehorst, Martijn, de Bruin, Alain, Bakker, Barbara M, Oosterveer, Maaike H, and van der Beek, Eline M

Published
2023

46. Endogenous Glucose Production in Patients With Glycogen Storage Disease Type Ia Estimated by Oral D-[6,6-2H2]-glucose.

Author

Rossi, Alessandro, Oosterveer, Maaike H, Dijk, Theo H van, Bleeker, Aycha, Koehorst, Martijn, Weinstein, David A, Bakker, Barbara M, and Derks, Terry G J

Subjects
GLYCOGEN storage disease, STABLE isotopes, METABOLIC disorders
Abstract

Context Glycogen storage disease type Ia (GSDIa) is an inborn metabolic disorder characterized by impaired endogenous glucose production (EGP). Monitoring of patients with GSDIa is prioritized because of ongoing treatment developments. Stable isotope tracers may enable reliable EGP monitoring. Objective The aim of this study was to prospectively assess the rate of appearance of endogenous glucose into the bloodstream (Ra) in patients with GSDIa after a single oral D-[6,6-2H2]-glucose dose. Methods Ten adult patients with GSDIa and 10 age-, sex-, and body mass index–matched healthy volunteers (HVs) were enrolled. For each participant, 3 oral glucose tracer tests were performed: (1) preprandial/fasted, (2) postprandial, and (3) randomly fed states. Dried blood spots were collected before D-[6,6-2H2]-glucose administration and 10, 20, 30, 40, 50, 60, 75, 90, and 120 minutes thereafter. Results Glucose Ra in fasted HVs was consistent with previously reported data. The time-averaged glucose Ra was significantly higher in (1) preprandial/fasted patients with GSDIa than HV and (2) postprandial HV compared with fasted HV(P <.05). A progressive decrease in glucose Ra was observed in preprandial/fasted patients with GSDIa; the change in glucose Ra time-course was directly correlated with the change in capillary glucose (P <.05). Conclusion This is the first study to quantify glucose Ra in patients with GSDIa using oral D-[6,6-2H2] glucose. The test can reliably estimate EGP under conditions in which fasting tolerance is unaffected but does not discriminate between relative contributions of EGP (eg, liver, kidney) and exogenous sources (eg, dietary cornstarch). Future application is warranted for longitudinal monitoring after novel genome based treatments in patients with GSDIa in whom nocturnal dietary management can be discontinued. [ABSTRACT FROM AUTHOR]

Published
2024
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47. Age and diet modulate the insulin-sensitizing effects of exercise: a tracer-based oral glucose tolerance test

Author

Vieira-Lara, Marcel A., primary, Reijne, Aaffien C., additional, Koshian, Serj, additional, Ciapaite, Jolita, additional, Abegaz, Fentaw, additional, Talarovicova, Alzbeta, additional, van Dijk, Theo H., additional, Versloot, Christian J., additional, Bandsma, Robert H.J., additional, Wolters, Justina C., additional, Groen, Albert K., additional, Reijngoud, Dirk-Jan, additional, van Dijk, Gertjan, additional, and Bakker, Barbara M., additional

Published
2023
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48. Hyperglycemia, pregnancy outcomes and maternal metabolic disease risk during pregnancy and lactation in a lean gestational diabetes mouse model

Author

Tol, Angela J.C., primary, Hribar, Kaja, additional, Kruit, Janine, additional, Bongiovanni, Laura, additional, Vieira‐Lara, Marcel A., additional, Koster, Mirjam H., additional, Kloosterhuis, Niels J., additional, Havinga, Rick, additional, Koehorst, Martijn, additional, de Bruin, Alain, additional, Bakker, Barbara M, additional, Oosterveer, Maaike H., additional, and van der Beek, Eline M., additional

Published
2023
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