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

Authors: 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.

Source: In eBioMedicine October 2023 96

Full humanization of the glycolytic pathway in Saccharomyces cerevisiae

Authors: Boonekamp, Francine J., Knibbe, Ewout, Vieira-Lara, Marcel A., Wijsman, Melanie, Luttik, Marijke A.H., van Eunen, Karen, Ridder, Maxime den, Bron, Reinier, Almonacid Suarez, Ana Maria, van Rijn, Patrick, Wolters, Justina C., Pabst, Martin, Daran, Jean-Marc, Bakker, Barbara M., Daran-Lapujade, Pascale

Source: In Cell Reports 28 June 2022 39(13)

Model-order reduction of biochemical reaction networks

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

Source: 2013 European Control Conference (ECC) Control Conference (ECC), 2013 European. :4502-4507 Jul, 2013

Relation: 2013 European Control Conference (ECC)

Precision-cut liver slices as an ex vivo model to assess impaired hepatic glucose production.

Authors: Kiyuna, Ligia Akemi, Krishnamurthy, Kishore Alagere, Homan, Esther B., Langelaar-Makkinje, Miriam, Gerding, Albert, Bos, Trijnie, Oosterhuis, Dorenda, Overduin, Ruben J., Schreuder, Andrea B., de Meijer, Vincent E., Olinga, Peter, Derks, Terry G. J., van Eunen, Karen, Bakker, Barbara M., Oosterveer, Maaike H.

Source: Communications Biology; 11/9/2024, Vol. 7 Issue 1, p1-13, 13p

Subject Terms: GLYCOGEN storage disease, INBORN errors of metabolism, GLUCOSE transporters, GLYCOGENOLYSIS, FORSKOLIN

Model-order reduction of biochemical reaction networks

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

Subject Terms: Computer Science - Systems and Control, Computer Science - Software Engineering, Mathematics - Dynamical Systems, Physics - Chemical Physics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1212.2438

Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids

Authors: Riemer, Pamela, Rydenfelt, Mattias, Marks, Matthias, van Eunen, Karen, Thedieck, Kathrin, Herrmann, Bernhard G., Blüthgen, Nils, Sers, Christine, Morkel, Markus

Source: Journal of cell biology. 216(6):1567-1578

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN611626719&indx=1&recIds=ETOCRN611626719

Precision-cut liver slices as an ex vivo model to assess impaired hepatic glucose production

Authors: Krishnamurthy, Kishore Alagere, Kiyuna, Ligia Akemi, Langelaar, Miriam, Gerding, Albert, Bos, Trijnie, Oosterhuis, Dorenda, Olinga, Peter, Van Eunen, Karen, Bakker, Barbara, Oosterveer, Maaike

Source: Journal of hepatology. 77(S1):S539-S540

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100169876690.0x000001&indx=1&recIds=ETOCvdc_100169876690.0x000001

The importance and challenges of in vivo-like enzyme kinetics

Authors: van Eunen, Karen, Bakker, Barbara M.

Source: In Perspectives in Science May 2014 1(1-6):126-130

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

Authors: den Besten, Gijs ^{*, †}, van Eunen, Karen ^{*, †}, Groen, Albert K. ^{*, †, §}, Venema, Koen ^{†, **}, Reijngoud, Dirk-Jan ^{*, †, §}, Bakker, Barbara M. ^{*, †}

Source: In Journal of Lipid Research September 2013 54(9):2325-2340

Personalised modelling of clinical heterogeneity between medium-chain acyl-CoA dehydrogenase patients.

Authors: Odendaal, Christoff, Jager, Emmalie A., Martines, Anne-Claire M. F., Vieira-Lara, Marcel A., Huijkman, Nicolette C. A., Kiyuna, Ligia A., Gerding, Albert, Wolters, Justina C., Heiner-Fokkema, Rebecca, van Eunen, Karen, Derks, Terry G. J., Bakker, Barbara M.

Source: BMC Biology; 9/4/2023, Vol. 21 Issue 1, p1-22, 22p

Subject Terms: ACYL coenzyme A, INBORN errors of metabolism, FATTY acid oxidation, PROTEOMICS, ASYMPTOMATIC patients

The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation.

Authors: Martines, Anne-Claire M. F.^1,2, Van Eunen, Karen^1,2, Reijngoud, Dirk-Jan^1,2, Bakker, Barbara M.^1,2 b.m.bakker01@umcg.nl

Source: PLoS Computational Biology. 4/3/2017, Vol. 13 Issue 4, p1-22. 22p.

Subject Terms: *FATTY acid oxidation, *ENERGY metabolism, *THIOLASES, *MITOCHONDRIAL proteins, *PROMISCUITY

Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders.

Authors: van Eunen, Karen^1,2, Volker-Touw, Catharina M. L.^1,3, Gerding, Albert¹, Bleeker, Aycha^1,2, Wolters, Justina C.^1,4, van Rijt, Willemijn J.⁵, Martines, Anne-Claire M. F.¹, Niezen-Koning, Klary E.⁶, Heiner, Rebecca M.⁶, Permentier, Hjalmar⁴, Groen, Albert K.^1,2,6,7, Reijngoud, Dirk-Jan^1,7, Derks, Terry G. J.⁵, Bakker, Barbara M.^1,7,8 b.m.bakker01@umcg.nl

Source: BMC Biology. 12/7/2016, Vol. 14, p1-15. 15p.

Subject Terms: *FATTY acid oxidation disorders, *BIOCHEMICAL substrates, *ACYL coenzyme A, *DEHYDROGENASES, *MITOCHONDRIA, *ENERGY metabolism

FRI298 - Precision-cut liver slices as an ex vivo model to assess impaired hepatic glucose production

Authors: Krishnamurthy, Kishore Alagere, Kiyuna, Ligia Akemi, Langelaar, Miriam, Gerding, Albert, Bos, Trijnie, Oosterhuis, Dorenda, Olinga, Peter, Van Eunen, Karen, Bakker, Barbara, Oosterveer, Maaike

Source: In Journal of Hepatology July 2022 77 Supplement 1:S539-S540

Molecular mechanisms of mTOR regulation by stress

Authors: Heberle, Alexander Martin, Prentzell, Mirja Tamara, van Eunen, Karen, Bakker, Barbara Marleen, Grellscheid, Sushma Nagaraja, Thedieck, Kathrin

Source: Molecular & cellular oncology. 2(2)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100058844428.0x000001&indx=1&recIds=ETOCvdc_100058844428.0x000001

Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload.

Authors: van Eunen, Karen^1,2, Simons, Sereh M. J.¹, Gerding, Albert^1,3, Bleeker, Aycha¹, den Besten, Gijs^1,2, Touw, Catharina M. L.¹, Houten, Sander M.⁴, Groen, Bert K.^1,2, Krab, Klaas⁵, Reijngoud, Dirk-Jan^1,2,3, Bakker, Barbara M.^1,2 b.m.bakker01@umcg.nl

Source: PLoS Computational Biology. Aug2013, Vol. 9 Issue 8, p1-8. 8p. 1 Diagram, 2 Graphs.

Subject Terms: *BIOCHEMICAL genetics, *METABOLIC disorders, *OXIDATION, *SYSTEMS biology, *ENZYMES, *OBESITY, *METABOLITES

Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics.

Authors: van Eunen, Karen^1,2,3, Kiewiet, Jose' A. L.^1,2, Westerhoff, Hans V.^1,2,4,5, Bakker, Barbara M.^1,2,3 b.m.bakker@med.umcg.nl

Source: PLoS Computational Biology. Apr2012, Vol. 8 Issue 4, p1-13. 13p.

Subject Terms: *BIOCHEMISTRY, *ENZYME kinetics, *METABOLISM, *BIOCHEMISTS, *GLYCOLYSIS, *GLUCOKINASE, *FUNGI

Measuring enzyme activities under standardized in vivo-like conditions for systems biology.

Authors: van Eunen, Karen^1,2, Bouwman, Jildau^1,2, Daran-Lapujade, Pascale^2,3, Postmus, Jarne⁴, Canelas, André B.^2,3, Mensonides, Femke I. C.^1,2, Orij, Rick⁴, Tuzun, Isil⁵, van den Brink, Joost^2,3, Smits, Gertien J.⁴, van Gulik, Walter M.^2,3, Brul, Stanley⁴, Heijnen, Joseph J.^2,3, de Winde, Johannes H.^2,3, de Mattos, M. J. Teixeira⁵, Kettner, Carsten⁶, Nielsen, Jens⁷, Westerhoff, Hans V.^1,2,8, Bakker, Barbara M.^1,2,9 B.M.Bakker@med.umcg.nl

Source: FEBS Journal. Feb2010, Vol. 277 Issue 3, p749-760. 12p. 4 Charts, 2 Graphs.

Subject Terms: *ENZYMES, *SYSTEMS biology, *ENZYME kinetics, *POTASSIUM, *SODIUM

Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker’s yeast.

Authors: van Eunen, Karen¹, Bouwman, Jildau^1,2, Lindenbergh, Alexander¹, Westerhoff, Hans V.^1,3, Bakker, Barbara M.^1,4 b.m.bakker@med.umcg.nl

Source: FEBS Journal. Oct2009, Vol. 276 Issue 19, p5521-5536. 16p. 4 Charts, 6 Graphs.

Subject Terms: *CELLULAR control mechanisms, *REGULATION of cell growth, *MALNUTRITION, *ENZYMOLOGY, *METABOLIC regulation, *GENE expression, *EDIBLE fungi, *FUNGI

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Simultaneous Induction of Glycolysis and Oxidative Phosphorylation during Activation of Hepatic Stellate Cells Reveals Novel Mitochondrial Targets to Treat Liver Fibrosis.

Authors: Smith-Cortinez, Natalia¹ (AUTHOR) natalia.fsc@gmail.com, van Eunen, Karen² (AUTHOR) k.van.eunen@umcg.nl, Heegsma, Janette¹ (AUTHOR) j.heegsma@umcg.nl, Serna-Salas, Sandra Alejandra¹ (AUTHOR) s.a.serna.salas@umcg.nl, Sydor, Svenja³ (AUTHOR) svenja.sydor@ruhr-uni-bochum.de, Bechmann, Lars P.³ (AUTHOR) lars.bechmann@rub.de, Moshage, Han¹ (AUTHOR) a.j.moshage@umcg.nl, Bakker, Barbara M.² (AUTHOR) b.m.bakker01@umcg.nl, Faber, Klaas Nico¹ (AUTHOR) k.n.faber@umcg.nl

Source: Cells (2073-4409). Nov2020, Vol. 9 Issue 11, p2456. 1p.

Subject Terms: *LIVER cells, *GLYCOLYSIS, *OXIDATIVE phosphorylation, *MITOCHONDRIAL DNA, *FIBROSIS, *LIVER