Peroxisome Interactions and Communication

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Researcher Declarations on Conformity
All ESRs are recruited
4.3 Awards of doctoral degrees

Awards of doctoral degrees. For universities with PhD programmes of 4 years (Netherlands and Belgium) and 4.5 years (Israel) this will be achieved only at months 54 and 60, respectively.

"4.2 Conference organisation ""Peroxisome Interactions and Communication"""

Conference organisation “Peroxisome Interactions and Communication”

4.1 Training School including scientific and transferable skills courses

Training Schools including scientific and transferable skills courses organized

PERICO vacancies advertised
5.1 Project website

Project website

5.5 Education Programme Report

Education Programme Report

5.6 Public dissemination of project results after protection

Public dissemination of project results after protection

Publications

Assessment of the Peroxisomal Redox State in Living Cells Using NADPH- and NAD+/NADH-Specific Fluorescent Protein Sensors

Auteurs: Cláudio F Costa Hongli Li Mohamed A F Hussein Yi Yang Celien Lismont Marc Fransen
Publié dans: Methods in Molecular Biology, Numéro 2643, 2023, Page(s) 183-197, ISBN 978-1-0716-3048-8
Éditeur: Humana
DOI: 10.1007/978-1-0716-3048-8_13

Isolation of Glycosomes from Trypanosoma brucei

Auteurs: Krishna, C.K., Franke, L., Erdmann, R., Kalel, V.C.
Publié dans: Methods in Molecular Biology book series (MIMB, volume 2643), 2023, ISBN 978-1-0716-3048-8
Éditeur: Humana, New York, NY
DOI: 10.1007/978-1-0716-3048-8_3

Identification of Peroxisome-Derived Hydrogen Peroxide-Sensitive Target Proteins Using a YAP1C-Based Genetic Probe

Auteurs: Celien Lismont Iulia Revenco Cláudio F Costa Hongli Li Mohamed A F Hussein Paul P Van Veldhoven Rita Derua Marc Fransen
Publié dans: Methods in Molecular Biology, Numéro 2643, 2023, Page(s) 161-181, ISBN 978-1-0716-3048-8
Éditeur: Humana
DOI: 10.1007/978-1-0716-3048-8_12

Applying CRISPR-Cas9 Genome Editing to Study Genes Involved in Peroxisome Biogenesis or Peroxisomal Functions

Auteurs: Chornyi S, Koster J, Waterham HR
Publié dans: Methods Mol Biol, Numéro 2643, 2023, Page(s) 233-245, ISBN 978-1-0716-3047-1
Éditeur: Humana, New York, NY
DOI: 10.1007/978-1-0716-3048-8_17

Analysis of Yeast Peroxisomes via Spatial Proteomics

Auteurs: Hirak Das, Alexandros Zografakis, Silke Oeljeklaus, Bettina Warscheid
Publié dans: Methods in Molecular Biology (Peroxisomes: Methods and protocols), Numéro Vol. 2643, 2023, Page(s) 13-31, ISBN 978-1-0716-3048-8
Éditeur: Humana
DOI: 10.1007/978-1-0716-3048-8_2

Peroxisomal Dysfunction and Oxidative Stress in Neurodegenerative Disease: A Bidirectional Crosstalk

Auteurs: Marc Fransen, Iulia Revenco, Hongli Li, Cláudio F. Costa, Celien Lismont, Paul P. Van Veldhoven
Publié dans: Peroxisome Biology: Experimental Models, Peroxisomal Disorders and Neurological Diseases, Numéro 1299, 2020, Page(s) 19-30, ISBN 978-3-030-60203-1
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-60204-8_2

Generation of Reporter Cell Lines for Endogenous Expression Analysis of Peroxisomal Proteins

Auteurs: Silva, Beatriz S. C.; Schrader, Tina A.; Schrader, Michael; Carmichael, Ruth E.
Publié dans: Methods Mol Biol, Numéro 2643, 2023, Page(s) 247-270, ISSN 1940-6029
Éditeur: Springer
DOI: 10.1007/978-1-0716-3048-8_18

Organoids as a model to study intestinal and liver dysfunction in severe malnutrition

Auteurs: José M. Horcas-Nieto, Christian J. Versloot, Miriam Langelaar-Makkinje, Albert Gerding, Tjasso Blokzijl, Mirjam H. Koster, Mirjam Baanstra, Ingrid A. Martini, Robert P. Coppes, Céline Bourdon, Sven C.D. van Ijzendoorn, Peter Kim, Robert H.J. Bandsma, Barbara M. Bakker
Publié dans: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Numéro 1869 (3), 2023, ISSN 0925-4439
Éditeur: Elsevier BV
DOI: 10.1016/j.bbadis.2022.166635

The Peroxisome-Autophagy Redox Connection: A Double-Edged Sword?

Auteurs: Hongli Li, Celien Lismont, Iulia Revenco, Mohamed A. F. Hussein, Cláudio F. Costa, Marc Fransen
Publié dans: Frontiers in Cell & Developmental Biology, 2021, Page(s) 1-16, ISSN 2296-634X
Éditeur: Frontiers Media S.A
DOI: 10.3389/fcell.2021.814047

The origin of long-chain fatty acids required for de novo ether lipid/plasmalogen synthesis.

Auteurs: Chornyi S, Ofman R, Koster J, Waterham HR
Publié dans: J Lipid Res, Numéro 100364, 2023, Page(s) In press, ISSN 1539-7262
Éditeur: American Society for Biochemistry and Molecular Biology
DOI: 10.1016/j.jlr.2023.100364

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

Auteurs: Ling C, Versloot CJ, Arvidsson Kvissberg ME, Hu G, Swain N, Horcas-Nieto JM, Miraglia E, Thind MK, Farooqui A, Gerding A, van Eunen K, Koster MH, Kloosterhuis NJ, Chi L, ChenMi Y, Langelaar-Makkinje M, Bourdon C, Swann J, Smit M, de Bruin A, Youssef SA, Feenstra M, van Dijk TH, Thedieck K, Jonker JW, Kim PK, Bakker BM, Bandsma RHJ
Publié dans: EBioMedicine, Numéro 96, 2023, Page(s) 104809, ISSN 2352-3964
Éditeur: Elsevier BV
DOI: 10.1016/j.ebiom.2023.104809

OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection

Auteurs: Marco Anteghini,Asmaa Haja,Vitor A.P. Martins dos Santos,Lambert Schomaker, Edoardo Saccentia
Publié dans: Computational and Structural Biotechnology Journal, Numéro 21, 2022, Page(s) 128-133, ISSN 2001-0370
Éditeur: ScienceDirect
DOI: 10.1016/j.csbj.2022.11.058

Towards automatization of organoid analysis: A deep learning approach to localize and quantify organoid images

Auteurs: Asmaa Haja, José M. Horcas-Nieto, Barbara M. Bakker, Lambert Schomaker
Publié dans: Computer Methods and Programs in Biomedicine Update, Numéro 3, 2023, ISSN 2666-9900
Éditeur: Elsevier BV
DOI: 10.1016/j.cmpbup.2023.100101

Insights Into the Peroxisomal Protein Inventory of Zebrafish

Auteurs: Kamoshita, Maki; Kumar, Rechal; Anteghini, Marco; Kunze, Markus; Islinger, Markus; Martins dos Santos, Vítor; Schrader, Michael
Publié dans: Frontiers in Physiology, 2022, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.822509

The peroxisome: an update on mysteries 3.0

Auteurs: Kumar, Rechal; Islinger, Markus; Worthy, Harley; Carmichael, Ruth; Schrader, Michael
Publié dans: Histochem Cell Biol, Numéro 161, 2024, Page(s) 99-132, ISSN 1432-119X
Éditeur: Springer
DOI: 10.1007/s00418-023-02259-5

Maintaining social contacts: The physiological relevance of organelle interactions

Auteurs: Beatriz S C Silva, Laura DiGiovanni, Rechal Kumar , Ruth E Carmichael, Peter K Kim, Michael Schrader
Publié dans: Biochim Biophys Acta Mol Cell Res, Numéro 1867(11):118800, 2020, ISSN 0167-4889
Éditeur: Elsevier BV
DOI: 10.1016/j.bbamcr.2020.118800

Differential roles for ACBD4 and ACBD5 in peroxisome–ER interactions and lipid metabolism

Auteurs: Joseph L. Costello, Janet Koster, Beatriz S.C. Silva, Harley L. Worthy, Tina A. Schrader, Christian Hacker, Josiah Passmore, Frans A. Kuypers, Hans R. Waterham, Michael Schrader
Publié dans: J Biol Chem, Numéro 299, 2023, Page(s) 105013, ISSN 1083-351X
Éditeur: Elsevier
DOI: 10.1016/j.jbc.2023.105013

Enhanced Levels of Peroxisome-Derived H2O2 Do Not Induce Pexophagy but Impair Autophagic Flux in HEK-293 and HeLa Cells

Auteurs: Hongli Li Celien Lismont Cláudio F Costa Mohamed A F Hussein Myriam Baes Marc Fransen
Publié dans: Antioxidants, Numéro 12 (613), 2023, Page(s) 1-21, ISSN 2076-3921
Éditeur: MDPI
DOI: 10.3390/antiox12030613

Peroxisome-Derived Hydrogen Peroxide Modulates the Sulfenylation Profiles of Key Redox Signaling Proteins in Flp-In T-REx 293 Cells

Auteurs: Celien Lismont, Iulia Revenco, Hongli Li, Cláudio F. Costa, Lisa Lenaerts, Mohamed A. F. Hussein, Jonas De Bie, Bernard Knoops, Paul P. Van Veldhoven, Rita Derua, Marc Fransen
Publié dans: Frontiers in Cell and Developmental Biology, Numéro 10:888873, 2022, Page(s) 1-19, ISSN 2296-634X
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fcell.2022.888873

Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay

Auteurs: Mira Rosenthal 1, Eyal Metzl-Raz 1, Jérôme Bürgi 2, Eden Yifrach 1, Layla Drwesh 3, Amir Fadel 1, Yoav Peleg 4, Doron Rapaport 3, Matthias Wilmanns 2 5, Naama Barkai 1, Maya Schuldiner 6, Einat Zalckvar 6
Publié dans: PNAS, Numéro 117 (35), 2020, Page(s) 21432-21440, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1920078117

Pex14p Phosphorylation Modulates Import of Citrate Synthase 2 Into Peroxisomes in Saccharomyces cerevisiae.

Auteurs: Andreas Schummer; Renate Maier; Shiran Gabay-Maskit; Tobias Hansen; Wignand W. D. Mühlhäuser; Ida Suppanz; Amir Fadel; Maya Schuldiner; Wolfgang Girzalsky; Silke Oeljeklaus; Silke Oeljeklaus; Einat Zalckvar; Ralf Erdmann; Bettina Warscheid; Bettina Warscheid
Publié dans: Frontiers in Cell and Developmental Biology, Numéro 20, 2020, ISSN 2296-634X
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fcell.2020.549451

Peroxisomal Hydrogen Peroxide Metabolism and Signaling in Health and Disease

Auteurs: Lismont, Revenco, Fransen
Publié dans: International Journal of Molecular Sciences, Numéro 20/15, 2019, Page(s) 3673, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20153673

DIMA: Data-Driven Selection of an Imputation Algorithm.

Auteurs: Janine Egert; Eva Brombacher; Bettina Warscheid; Clemens Kreutz
Publié dans: Journal of Proteome Research, Numéro 20, 2021, ISSN 1535-3893
Éditeur: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00119

Molecular basis of the glycosomal targeting of PEX11 and its mislocalization to mitochondrion in trypanosomes

Auteurs: Krishna, Chethan K.; Schmidt, Nadine; Tippler, Bettina G.; Schliebs, Wolfgang; Jung, Martin; Winklhofer, Konstanze F.; Erdmann, Ralf; Kalel, Vishal C.
Publié dans: Frontiers Cell and Developmental Biology, Numéro 1, 2023, ISSN 2296-634X
Éditeur: Frontiers Media SA
DOI: 10.3389/fcell.2023.1213761

Peroxisomal Metabolite and Cofactor Transport in Humans.

Auteurs: Chornyi S, IJlst L, van Roermund CWT, Wanders RJA, Waterham HR
Publié dans: Front Cell Dev Biol, Numéro 8, 2021, Page(s) 613892, ISSN 2296-634X
Éditeur: Frontiers Media SA
DOI: 10.3389/fcell.2020.613892

A Fully Automated End-to-End Process for Fluorescence Microscopy Images of Yeast Cells: From Segmentation to Detection and Classification

Auteurs: Asmaa Haja, Lambert Schomaker
Publié dans: Proceedings of 2021 International Conference on Medical Imaging and Computer-Aided Diagnosis (MICAD 2021), 2021, Page(s) 10, ISBN 978-981-16-3880-0
Éditeur: Springer
DOI: 10.1007/978-981-16-3880-0_5

A Comparison of Different U-Net Models for Segmentation of Overlapping Organoids

Auteurs: Marco Anteghini, Asmaa Haja, Vitor AP Martins dos Santos, Lambert Schomaker, Edoardo Saccenti
Publié dans: ICBBE '22: Proceedings of the 2022 9th International Conference on Biomedical and Bioinformatics Engineering, 2022, Page(s) 1-10
Éditeur: Association for Computing Machinery (ACM)
DOI: 10.1145/3574198.3574199

Finding Balance: A series of U-Net models forImage Segmentation of Overlapping organoids

Auteurs: Stefania Radu, Asmaa Haja, Lambert Schomaker
Publié dans: 2022, Page(s) 1-19
Éditeur: University of Groningen

OrganelX Web Server for Sub-Peroxisomal and Sub-Mitochondrial protein localisation

Auteurs: Marco Anteghini, Asmaa Haja, Vitor AP Martins dos Santos, Lambert Schomaker, Edoardo Saccenti
Publié dans: 2022
Éditeur: bioRxiv
DOI: 10.1101/2022.06.21.497045

PEX1 is essential for the glycosome biogenesis and trypanosomatid parasite survival

Auteurs: Mahadevan, Lavanya; Arya, Hemant; Schliebs, Wolfgang; Erdmann, Ralf; Kalel, Vishal C.
Publié dans: BioRxiv, Numéro 21, 2023, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.05.550684

Unravelling the molecular mechanisms of peroxisome-organelle communication and interplay

Auteurs: Beatriz Silva
Publié dans: 2023
Éditeur: University of Exeter

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