Sort by
Showing 21 to 30 of 2,331 entries
Show entries

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},
}

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
}

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
}

Xinyi Yang, Teresa Ferraro, Kelly Molnar, Julien Pontabry, Sam-Rayden Malanda, Nicola Maghelli, Loic Royer, Stephan W. Grill, Gene Myers, Silvia Grigolon, Michel Labouesse
Repeated extrinsic and anisotropic mechanical inputs promote C. elegans polarized adherens junction elongation.
Dev Cell, 60(20) 2777-2790 (2025)
Open Access PubMed Source   

A key challenge in development is understanding how complex organisms physically coordinate the morphogenesis of multiple tissues. Here, using biophysical approaches, we investigate how muscles under the epidermis specifically stimulate the extension of anterior-posterior (AP)-oriented epidermal adherens junctions during late C. elegans embryonic elongation. First, light-sheet imaging shows that asynchronous patterns of muscle contractions drive embryo rotations. In turn, junctions between the lateral and dorso-ventral epidermis repeatedly oscillate between a folded, hypotensed state and an extended, hypertensed state. Second, fluorescence recovery after photobleaching (FRAP) analysis of an E-cadherin::GFP construct shows that muscle contractions stimulate E-cadherin turnover. Moreover, a mechano-chemical model backed by genetic tests suggests that E-cadherin trafficking controls junction elongation due to lower line tension. Altogether, our results illustrate how muscle contractions fluidize epidermal adherens junctions, which, combined with anisotropic tension in the epidermis, drive their polarized extension.
@article{Yang9021,
author={Xinyi Yang, Teresa Ferraro, Kelly Molnar, Julien Pontabry, Sam-Rayden Malanda, Nicola Maghelli, Loic Royer, Stephan W. Grill, Gene Myers, Silvia Grigolon, Michel Labouesse},
title={Repeated extrinsic and anisotropic mechanical inputs promote C. elegans polarized adherens junction elongation.},
journal ={Developmental cell},
volume={60},
issue ={20},
pages={2777--2790},
year=2025
}

Meritxell Huch, Saanjbati Adhikari
An interview with Meritxell (Meri) Huch.
Development, 152(20) Art. No. dev205227 (2025)
PubMed Source   

Meritxell (Meri) Huch is a Director and Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics, Germany, where her group uses 3D organoid models to study the maintenance and repair of adult tissues, as well as the mechanisms by which their dysregulation contributes to disease. This year, Meri is a Guest Editor for Development's special issue on lifelong development, which highlights how developmental processes and pathways are used throughout animal lifespans. We caught up with Meri over Teams to discuss the importance of using organoid models to study tissue regeneration and pathology, as well as some of the most exciting research questions that her lab is trying to answer.
@article{Huch9072,
author={Meritxell Huch, Saanjbati Adhikari},
title={An interview with Meritxell (Meri) Huch.},
journal ={Development (Cambridge, England)},
volume={152},
issue ={20},
pages={null--null},
year=2025
}
* joint first authors, # joint corresponding authors