Polymers in the Liver: Metabolism and Regulation

Deliverables

Abstracts dissemination conference online
Course Material Online
PoLiMeR website online

Final report on dissemination, exploitation, and outreach

Final report on dissemination exploitation and outreach

Identification of modules suitable for e-learning

Identification of modules suitable for elearning

Establishment of Supervisory Board
Completion of doctoral programmes

Completion of doctoral programmes for ESRs in a 3 year PhD programme. Note that PhD students in a 4 year programme will finish only a year after PoLiMeR ends.

Introduction Course + 4 Advanced Training Courses

Introduction Course 4 Advanced Training Courses

Project data and models publicly available
5 Progress Workshops
Researcher Declarations on Conformity
5 Transferable Skills Modules
Final dissemination conference

Publications

Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

Author(s): Burak Yulug, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Halil Aziz Velioglu, Hong Yang, Ebru Coskun, Ezgi Idil, Rahim Nogaylar, Ahmet Ozsimsek, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Ahmet Hacimuftuoglu, Serkan Yildirim, Muhammad Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Borén, Mathias Uhlén & Adil Mardinoglu
Published in: Translational Neurodegeneration, 2023, ISSN 2047-9158
Publisher: Springer Nature
DOI: 10.1186/s40035-023-00336-2

Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis

Author(s): Mujdat Zeybel, Muhammad Arif, Xiangyu Li, Ozlem Altay, Hong Yang, Mengnan Shi, Murat Akyildiz, Burcin Saglam, Mehmet Gokhan Gonenli, Buket Yigit, Burge Ulukan, Dilek Ural, Saeed Shoaie, Hasan Turkez, Jens Nielsen, Cheng Zhang, Mathias Uhlén, Jan Borén, Adil Mardinoglu
Published in: Advanced Science, 2022, ISSN 2198-3844
Publisher: Wiley-VCH GmbH
DOI: 10.1002/advs.202104373

In vitro grafting of hepatic spheroids and organoids on a microfluidic vascular bed

Author(s): Flavio Bonanini; Dorota Kurek; Sara Previdi; Arnaud Nicolas; Delilah Hendriks; Sander de Ruiter; Marine Meyer; Maria Clapés Cabrer; Roelof Dinkelberg; Silvia Bonilla García; Bart Kramer; Thomas Olivier; Huili Hu; Carmen López-Iglesias; Frederik Schavemaker; Erik Walinga; Devanjali Dutta; Karla Queiroz; Karel Domansky; Bob Ronden; Jos Joore; Henriette L. Lanz; Peter J. Peters; Sebastiaan J. Trie
Published in: Angiongenesis, Issue 25, 2022, Page(s) 455-470, ISSN 0969-6970
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10456-022-09842-9

Normalization of hepatic ChREBP activity does not protect against liver disease progression in a mouse model for Glycogen Storage Disease type Ia

Author(s): Martijn G. S. Rutten, Yu Lei, Joanne H. Hoogerland, Vincent W. Bloks, Hong Yang, Trijnie Bos, Kishore A. Krishnamurthy, Aycha Bleeker, Mirjam H. Koster, Rachel E. Thomas, Justina C. Wolters, Hilda van den Bos, Gilles Mithieux, Fabienne Rajas, Adil Mardinoglu, Diana C. J. Spierings, Alain de Bruin, Bart van de Sluis & Maaike H. Oosterveer
Published in: Cancer & Metabolism, 2023, ISSN 2049-3002
Publisher: Springer Nature
DOI: 10.1186/s40170-023-00305-3

Finding new edges: systems approaches to MTOR signaling

Author(s): Alexander Martin Heberle, Ulrike Rehbein, Maria Rodríguez Peiris, Kathrin Thedieck
Published in: Biochemical Society Transactions, 2021, ISSN 0300-5127
Publisher: Portland Press, Ltd.
DOI: 10.1042/bst20190730

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII

Author(s): Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu
Published in: Database, 2023, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baad005

Hepatic ChREBP orchestrates intrahepatic carbohydrate metabolism to limit hepatic glucose 6-phosphate and glycogen accumulation in a mouse model for acute Glycogen Storage Disease type Ib

Author(s): K.A. Krishnamurthy, M.G.S. Rutten, J.A. Hoogerland, T.H. Van Dijk, T. Bos, M. Koehorst, M.P. De Vries, N.J. Kloosterhuis, H. Havinga, B.V. Schomakers, M. van Weeghel, J.C. Wolters, B.M. Bakker, M.H. Oosterveer
Published in: Molecular Metabolism, 2023, ISSN 2212-8778
Publisher: Elsevier GmbH
DOI: 10.1016/j.molmet.2023.101838

Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme

Author(s): Yvan Rousset, Oliver Ebenhöh, Adélaïde Raguin
Published in: PLOS Computational Biology, 2023, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1010694

A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease

Author(s): Yang H., Arif M., Yuan M., Li X., Shong K., Türkez H., Nielsen J., Uhlén M., Borén J., Zhang C., Mardinoglu A.
Published in: iScience, 2021, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2021.103222

Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators

Author(s): Hong Yang, Xiangyu Li, Han Jin, Hasan Turkez, Gurkan Ozturk, Hamdi Levent Doganay, Cheng Zhang, Jens Nielsen, Mathias Uhlén, Jan Borén, Adil Mardinoglu
Published in: Free Radical Biology and Medicine, 2023, ISSN 0891-5849
Publisher: Elsevier BV
DOI: 10.1016/j.freeradbiomed.2023.05.013

Kinetic data for modeling the dynamics of the enzymes involved in animal fatty acid synthesis

Author(s): Chilperic Armel Foko Kuate, Oliver Ebenhöh, Barbara M. Bakker, Adélaïde Raguin
Published in: Bioscience Reports, 2023, ISSN 0144-8463
Publisher: Kluwer Academic Publishers
DOI: 10.1042/bsr20222496

Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients

Author(s): Mujdat Zeybel, Ozlem Altay, Muhammad Arif, Xiangyu Li, Hong Yang, Claudia Fredolini, Murat Akyildiz, Burcin Saglam, Mehmet Gokhan Gonenli, Dilek Ural, Woonghee Kim, Jochen M Schwenk, Cheng Zhang, Saeed Shoaie, Jens Nielsen, Mathias Uhlén, Jan Borén, Adil Mardinoglu
Published in: Molecular Systems Biology, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110459

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

Author(s): Christoff Odendaal, Emmalie A. Jager, Anne-Claire M. F. Martines, Marcel A. Vieira-Lara, Nicolette C. A. Huijkman, Ligia A. Kiyuna, Albert Gerding, Justina C. Wolters, Rebecca Heiner-Fokkema, Karen van Eunen, Terry G. J. Derks & Barbara M. Bakker
Published in: BMC Biology, 2023, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-023-01652-9

Thermodynamic Limits and Optimality of Microbial Growth

Author(s): Nima Saadat, Tim Nies, Yvan Rousset, Oliver Ebenhöh
Published in: Entropy, Issue 22/3, 2020, Page(s) 277, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e22030277

Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

Author(s): St. Elmo Wilken, Mathieu Besançon, Miroslav Kratochvíl, Chilperic Armel Foko Kuate, Christophe Trefois, Wei Gu, Oliver Ebenhöh
Published in: Metabolic Engineering, 2022, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2022.09.002

Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet

Author(s): Hong Yang, Jordi Mayneris-Perxachs, Noemí Boqué, Josep M. del Bas, Lluís Arola, Meng Yuan, Hasan Türkez, Mathias Uhlén, Jan Borén, Cheng Zhang, Adil Mardinoglu and Antoni Caimari
Published in: Biomedicines, 2021, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines9101440

Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19.

Author(s): Ozlem Altay; Ozlem Altay; Muhammad Arif; Xiangyu Li; Hong Yang; Mehtap Aydin; Gizem Alkurt; Woong-Hee Kim; Dogukan Akyol; Cheng Zhang; Cheng Zhang; Gizem Dinler-Doganay; Hasan Turkez; Saeed Shoaie; Saeed Shoaie; Jens Nielsen; Jan Borén; Oktay Olmuscelik; Levent Doganay; Mathias Uhlén; Adil Mardinoglu; Adil Mardinoglu
Published in: Advanced Science, Issue 8 (17), 2021, ISSN 2198-3844
Publisher: Wiley
DOI: 10.1002/advs.202101222

Development of HILIC-MS/MS method for acyl-CoAs covering short- to long-chain species in a single analytical run

Author(s): Madhulika Singh, Ligia Akemi Kiyuna, Christoff Odendaal, Barbara M. Bakker, Amy C Harms Author
Published in: ChemRxiv, 2023, ISSN 2573-2293
Publisher: Cambridge Unvisersity Press
DOI: 10.26434/chemrxiv-2023-h0w52

Deliverables

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