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Lucas de Oliveira Petrocchi Ribas
Scaling of BMP signaling gradients during zebrafish pectoral fin growth in development and regeneration.
Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2025)
 

@phdthesis{deOliveiraPetrocchiRibas9090,
author = {Lucas de Oliveira Petrocchi Ribas },
title={Scaling of BMP signaling gradients during zebrafish pectoral fin growth in development and regeneration.},
school = {Technische Universität Dresden},
year=2025,
address = {Dresden, Germany},
}

Anna Körte
Spatial patterning of mitochondrial metabolism during early vertebrate development.
Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2025)
 

@phdthesis{Körte9089,
author = {Anna Körte},
title={Spatial patterning of mitochondrial metabolism during early vertebrate development.},
school = {Technische Universität Dresden},
year=2025,
address = {Dresden, Germany},
}

Kristin Böhlig, Juan M Iglesias-Artola, Antonino Asaro, Hjoerdis Mathilda Lennartz, Anna C Link, Björn Drobot, André Nadler
Bifunctional Probes Reveal the Rules of Intracellular Ether Lipid Transport.
Angew Chem Int Ed Engl, 64(46) Art. No. e202513360 (2025)
Open Access PubMed Source   

Ether glycerophospholipids bear a long chain alcohol attached via an alkyl or vinyl ether bond at the sn1 position of the glycerol backbone. Ether lipids play a significant role in physiology and human health. However, their cellular functions remain largely unknown due to a lack of tools for identifying their subcellular localization and interacting proteins. Here, we address this methodological gap by synthesizing minimally modified bifunctional ether lipid probes by introducing diazirine and alkyne groups. To interrogate the subcellular kinetics of intracellular ether lipid transport in mammalian cells, we used a combination of fluorescence imaging, machine learning-assisted image analysis, and mathematical modelling. We find that alkyl-linked ether lipids are transported up to twofold faster than vinyl-linked species (plasmalogens), pointing to yet undiscovered cellular lipid transport machinery able to distinguish between linkage types differing by as little as two hydrogen atoms. We find that ether lipid transport predominantly occurs via non-vesicular pathways, with varying contributions from vesicular mechanisms between cell types. Altogether, our results suggest that differential recognition of alkyl- and vinyl ether lipids by lipid transfer proteins contributes to their distinct biological functions. In the future, the probes reported here will enable studying ether lipid biology in much greater detail through identification of interacting proteins and in-depth characterization of intracellular ether lipid dynamics.
@article{Böhlig9058,
author={Kristin Böhlig, Juan M Iglesias-Artola, Antonino Asaro, Hjoerdis Mathilda Lennartz, Anna C Link, Björn Drobot, André Nadler},
title={Bifunctional Probes Reveal the Rules of Intracellular Ether Lipid Transport.},
journal ={Angewandte Chemie (International ed. in English)},
volume={64},
issue ={46},
pages={null--null},
year=2025
}

Ksenia Kuznetsova*, Maxim Scheremetjew*, Jialin Yin, HongKee Moon, Diego A Vargas, Anna Hadarovich, Natasha Steffi Lewis, Carsten Hoege, Chi Fung Willis Chow, David Kuster, Jik Nijssen, Alberto Hernandez-Armendariz, Jonathan C Savage, Yu Wei, Silja Zedlitz, Hari Raj Singh, Soumyadeep Ghosh, Allysa P Kemraj, Lena Hersemann, Anthony Hyman, Diana M Mitrea#, Agnes Toth-Petroczy#
CD-CODE 2.0: an enhanced condensate knowledgebase integrating pathobiology, condensate modulating drugs, and host-pathogen interactions.
Nucleic Acids Res, Art. No. doi: 10.1093/nar/gkaf1104 (2025)
Open Access PubMed Source   

CD-CODE 2.0 (https://cd-code.org) is an enhanced web application and database of condensates, expanding the utility of version 1.0 for biomedical research. New features include data on nucleic acids condensate components, infectious condensates, condensate modulating drugs, and disease-linked condensates. Enhanced search functions, programmatic access, and relational architecture enable interconnectivity across major biomedical databases (e.g. condensates, proteins, chemistry, and disease), fostering systems-level insights and accelerating hypothesis generation and therapeutic discovery through the lens of condensate biology.
@article{Kuznetsova9085,
author={Ksenia Kuznetsova, Maxim Scheremetjew, Jialin Yin, HongKee Moon, Diego A Vargas, Anna Hadarovich, Natasha Steffi Lewis, Carsten Hoege, Chi Fung Willis Chow, David Kuster, Jik Nijssen, Alberto Hernandez-Armendariz, Jonathan C Savage, Yu Wei, Silja Zedlitz, Hari Raj Singh, Soumyadeep Ghosh, Allysa P Kemraj, Lena Hersemann, Anthony Hyman, Diana M Mitrea, Agnes Toth-Petroczy},
title={CD-CODE 2.0: an enhanced condensate knowledgebase integrating pathobiology, condensate modulating drugs, and host-pathogen interactions.},
journal ={Nucleic acids research},
volume={},
pages={1--1},
year=2025
}

Sophie Achilles, Jan-Niklas Tomczak, Fabiane-Samira Baumann, Bassam G Haddad, Stefan Oswald, Jan-Philipp Machtens, Eric R Geertsma, Ilka Wittig, Georg Lamprecht
N-glycans on SLC26A3 do not significantly alter plasma membrane or lipid raft trafficking, but appear to stabilize interdomain contacts to stimulate transport.
Am J Physiol Gastrointest Liver Physiol, 329(5) 628-638 (2025)
Open Access PubMed Source   

DRA (Downregulated in adenoma, SLC26A3) is a major apical intestinal Cl-/HCO3- exchanger, which is expressed in complex and hybrid N-glycosylated forms. Although the importance of N-glycosylation is evident from the significantly reduced transport activity of non-N-glycosylated DRA constructs (DRA-N0), the underlying molecular mechanisms are controversial. Therefore, plasma membrane expression and lipid raft localization of glycosylation-deficient DRA-N0 were analyzed in HEK cells. The activity of DRA-N0 was reduced by 70% compared with the wild-type construct. Absolute expression of DRA-N0 was significantly reduced by ∼57% in the cell lysate and by 34 and 45% in the plasma membrane and in plasma membrane-derived lipid rafts, respectively. These amounts are insufficient to account for the reduction in activity. Furthermore, the statistical analysis did not support a difference in the relative expression of DRA and DRA-N0 in the plasma membrane and in plasma membrane-derived lipid rafts, indicating that N-glycosylation does not affect transport activity through trafficking and localization in these cell compartments. To gain insight into potential intramolecular effects of N-glycosylation on DRA, its three-dimensional structure was predicted using AlphaFold3 with complex N-glycans covalently attached to N153, N161, and N164 in the transport domain. This revealed multiple inward- and outward-facing conformations of the protein. The number of interdomain contacts of the transport domain-bound glycans with the scaffold domain was higher in the inward-facing state. Because substrate release to the cytoplasm represents the rate-limiting step in many transport proteins, this suggests that in DRA, glycans stabilize the inward-facing state facilitating anion transport.NEW & NOTEWORTHY Deficient N-glycosylation decreases DRA transport activity but does not significantly affect trafficking to the plasma membrane or to lipid rafts. Meanwhile, molecular modeling predicts stabilizing interdomain contacts of the glycans, covalently attached to the transport domain, with the scaffold domain having more contacts in the inward-facing state. Favoring the inward-facing state may facilitate more efficacious anion transport, as substrate release from this state into the cytoplasm is a rate limiting step for numerous transport proteins.
@article{Achilles9069,
author={Sophie Achilles, Jan-Niklas Tomczak, Fabiane-Samira Baumann, Bassam G Haddad, Stefan Oswald, Jan-Philipp Machtens, Eric R Geertsma, Ilka Wittig, Georg Lamprecht},
title={N-glycans on SLC26A3 do not significantly alter plasma membrane or lipid raft trafficking, but appear to stabilize interdomain contacts to stimulate transport.},
journal ={American journal of physiology. Gastrointestinal and liver physiology},
volume={329},
issue ={5},
pages={628--638},
year=2025
}

Jessica Thiel, Duran Sürün, Desiree C Brändle, Madeleine Teichert, Stephan R Künzel, Ulrike Friedrich, Andreas Dahl, Kristin Schubert, Ignacy Rzagalinski, Andrej Shevchenko, Sofia Traikov, Peter Mirtschink, Lisa Wagenführ, Frank Buchholz, Kristina Hölig, Torsten Tonn, Romy Kronstein-Wiedemann
Knock Out of miRNA-30a-5p and Reconstitution of the Actin Network Dynamics Partly Restores the Impaired Terminal Erythroid Differentiation during Blood Pharming.
Stem Cell Rev Rep, 21(8) 2637-2653 (2025)
Open Access PubMed Source   

In vitro red blood cell (RBC) production offers a promising complement to conventional blood donation, particularly for patients with rare blood types. Previously, we developed imBMEP-A, the first erythroid cell line derived from reticulocyte progenitors, which maintains robust hemoglobin expression and erythroid differentiation in the presence of erythropoietin (EPO) despite its immortalized state. However, clinical translation remains hindered by the inability to scale up production due to impaired in vitro enucleation of RBC progenitor cell lines. Enhancing enucleation efficiency in imBMEP-A cells involved CRISPR/Cas9-mediated knockout (K.O.) of miR-30a-5p, a key enucleation inhibitor, moderately increasing rates to 3.3 ± 0.4%- 8.9 ± 1.7%. Further investigation of enucleation inefficiencies led to transcriptome and proteome comparisons between imBMEP-miR30a-K.O. cells and hematopoietic stem cells (HSCs). These analyses revealed altered gene expression and protein abundances linked to metabolic transitions, apoptosis promotion, and cytoskeletal regulation. Notably, forced expression of the proto-oncogene c-Myc, required for cell immortalization, emerged as a key driver of these physiological changes. Counteracting these effects required optimization of imBMEP-A cells by activating BCL-XL transcription and knocking out SCIN, which encodes the actin-severing protein scinderin. While BCL-XL is upregulated in normal erythropoiesis, it is downregulated in imBMEP-A. Conversely, SCIN, typically absent in erythroid cells, is highly expressed in imBMEP-A, disrupting actin organization. These interventions improved viability, restored actin network formation, and increased terminal erythropoiesis, yielding 22.1 ± 1.7% more orthochromatic erythroblasts. These findings establish a foundation for optimizing imBMEP-A cells for therapeutic use and advancing the understanding the pathophysiology of erythroleukemia.
@article{Thiel9053,
author={Jessica Thiel, Duran Sürün, Desiree C Brändle, Madeleine Teichert, Stephan R Künzel, Ulrike Friedrich, Andreas Dahl, Kristin Schubert, Ignacy Rzagalinski, Andrej Shevchenko, Sofia Traikov, Peter Mirtschink, Lisa Wagenführ, Frank Buchholz, Kristina Hölig, Torsten Tonn, Romy Kronstein-Wiedemann},
title={Knock Out of miRNA-30a-5p and Reconstitution of the Actin Network Dynamics Partly Restores the Impaired Terminal Erythroid Differentiation during Blood Pharming.},
journal ={Stem cell reviews and reports},
volume={21},
issue ={8},
pages={2637--2653},
year=2025
}

Olivier N Lemaire*#, Mélissa Belhamri*, Anna Shevchenko, Tristan Wagner#
Carbon-monoxide-driven bioethanol production operates through a tungsten-dependent catalyst.
Nat Chem Biol, Art. No. doi: 10.1038/s41589-025-02055-3 (2025)
Open Access PubMed Source   

Microbial alcohol production from waste gases is a game changer for sustainable carbon cycling and remediation. While the biotechnological process using Clostridium autoethanogenum to transform syngas (H2, CO2 and CO) is blooming, scientific debates remain on the ethanol biosynthesis pathway. Here, we experimentally validated that ethanol production is initiated through a tungsten-dependent aldehyde:ferredoxin oxidoreductase (AFOR), which reduces acetate to acetaldehyde. The reaction, thermodynamically unfavorable under standard conditions, has been considered by many as unsuitable in vivo but is rather approved by metabolic modeling. To answer this riddle, we demonstrated that the thermodynamic coupling of CO oxidation and ethanol synthesis allows acetate reduction. The experiments, performed with native CO dehydrogenase and AFOR, highlighted the key role of ferredoxin in stimulating the activity of both metalloenzymes and electron shuttling. The crystal structure of holo AFOR, refined to 1.59-Å resolution, and its biochemical characterization provide new insights into the cofactor chemistry and the specificities of this enzyme, fundamental to sustainable biofuel production.
@article{Lemaire9080,
author={Olivier N Lemaire, Mélissa Belhamri, Anna Shevchenko, Tristan Wagner},
title={Carbon-monoxide-driven bioethanol production operates through a tungsten-dependent catalyst.},
journal ={Nature chemical biology},
volume={},
pages={1--1},
year=2025
}

Meritxell Huch#, Mansi Srivastava#, Alex Eve
Beyond the beginning - development that lasts a lifetime.
Development, 152(20) Art. No. dev205313 (2025)
PubMed Source  

@article{Huch9079,
author={Meritxell Huch, Mansi Srivastava, Alex Eve},
title={Beyond the beginning - development that lasts a lifetime.},
journal ={Development (Cambridge, England)},
volume={152},
issue ={20},
pages={null--null},
year=2025
}

David Kuster
Hyperphosphorylation of the CoV-2 nucleocapsid protein governs viral genome packaging.
Ph.D. Thesis, Technische Universität Dresden, Dresden, Germany (2025)
 

@phdthesis{Kuster9088,
author = {David Kuster},
title={Hyperphosphorylation of the CoV-2 nucleocapsid protein governs viral genome packaging.},
school = {Technische Universität Dresden},
year=2025,
address = {Dresden, Germany},
}

Max Rosenkranz, Markus Kaestner, Ivo F. Sbalzarini
Data-Efficient Inverse Design of Spinodoid Metamaterials.
INTEGRATING MATERIALS AND MANUFACTURING INNOVATION, Art. No. doi: 10.1007/s40192-025-00426-1 (2025)
Open Access Source   

We present a data-efficient neural-network model for predicting linear-elastic properties of spinodoid metamaterials from their mesoscale structure. Our machine-learning model requires 75 data points for training, greatly improving data efficiency over previous models that required thousands of training samples. We achieve this by leveraging concepts from geometric learning. Specifically, we exploit physical properties, such as positive semi-definiteness of the elasticity tensor, as well as structural invariances and equivariances of the problem, for example with respect to coordinate axes permutations. The neural network model is designed to exactly fulfill these constraints; it does not have to learn them from data. The resulting model enables data- and compute-efficient inverse design of spinodoid metamaterials. In inverse design, the goal is to find a material mesostructure that leads to desired mechanical properties on the macroscale. Exactly fulfilling physical and structural constraints, the present neural network model remains differentiable. This allows using fast gradient-based optimizers for inverse design. We demonstrate this by inversely designing spinodoid metamaterials that achieve desired linear elastic target properties in three dimensions. Inverse design is treated as a constrained optimization problem over the parameters describing the metamaterial. The results confirm that the present approach requires significantly less training data than previous machine-learning approaches and allows incorporating multiple objectives in the inverse design process. Since the structure of the design space is independent of the target material properties, we hope that such data-efficient models will be useful also for inverse design of spinodoids beyond linear elasticity.
@article{Rosenkranz9081,
author={Max Rosenkranz, Markus Kaestner, Ivo F. Sbalzarini},
title={Data-Efficient Inverse Design of Spinodoid Metamaterials.},
journal ={INTEGRATING MATERIALS AND MANUFACTURING INNOVATION},
volume={},
pages={1--1},
year=2025
}
* joint first authors, # joint corresponding authors