Biology subjects

Lommel, M.

Publications and source records attributed to Lommel, M..

5 recordsLinked to original sources

bioRxiv2025

POMT-dependent O-mannosylation regulates integrin β1 maturation via N-glycan processing

Withdrawal StatementThe authors have withdrawn this manuscript because following a careful internal review conducted in the course of manuscript revision, the authors identified that parts of the presented data could not be reliably traced back to the corresponding original datasets in their current form. While the general biological interpretation is not necessarily invalidated by this finding, the integrity of the present data representation no longer meets the standard required for publication. For this reason, the authors have decided to withdraw this preprint and will refrain from pursuing publication until the underlying data situation has been fully clarified and, if possible, reconstructed. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The authors regret any inconvenience caused to the scientific community.

cell biology↗

bioRxiv2024

The conserved membrane-proximal domain of Sbh1/ Sec61β guides signal peptides into the Sec61 channel

In eukaryotes, protein secretion begins with protein translocation through the universally conserved Sec61 channel into the endoplasmic reticulum (ER). Its {beta}-subunit, Sbh1 in yeast, enhances ER import of proteins with specific suboptimal signal peptides by an unknown mechanism. The Sbh1 cytosolic N-terminus consists of an intrinsically disordered, non-conserved region (IDR) that has never been visualized in active channel structures, but is close to the translocating polypeptide in the cytosolic channel vestibule. The Sbh1/Sec61{beta} N-terminal IDR is followed by structured 15 amino acids and its C-terminal transmembrane helix, both of which are conserved. We show here that the proline and adjacent conserved residues at the Sbh1 cytosolic/transmembrane domain interface form a hinge that positions the Sbh1 cytosolic domain across the channel vestibule and orients it with respect to the lateral gate. This orientation is critical for Sbh1-dependent protein insertion into the channel. Sbh1-dependence of Sec61 channel insertion is a function of the signal peptide of the respective secretory protein. By chemical crosslinking of purified cytosolic domains of Sbh1 and its paralog Sbh2 to synthetic signal peptides derived from their respective client proteins, we show that the cytosolic domains of Sbh1 and Sbh2 contain specific signal peptide binding sites. The position of the crosslinked residues suggests that signal peptide binding is mediated by the IDRs. We conclude that Sec61{beta} homologs directly recognize signal peptides of their substrates and guide them into the Sec61 channel; they thus control entry of specific proteins into the secretory pathway.

biochemistry↗

bioRxiv2021

SPIRO-the automated Petri plate imaging platform designed by biologists, for biologists

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photos of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIROs excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared to manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing and photoblastic response.

plant biology↗

bioRxiv2021

β-Catenin and canonical Wnts control two separate pattern formation systems in Hydra: Insights from mathematical modelling

The formation of body axes and apical termini is crucial for animal development. In Hydra, nuclear {beta}-catenin and Wnt3 play key roles and were previously thought to be part of a single mechanism for axis and head formation. This study challenges this view by combining mathematical modeling with experimental data. We show that {beta}-catenin and Wnt3 patterning in Hydra operate at two different scales, requiring distinct inhibitory mechanisms. {beta}-catenin, possibly interacting with other Wnts, co-ordinates axis formation, whereas Wnt3 is involved in small-scale head patterning. A double-loop reaction-diffusion model was developed, demonstrating the ability to describe patterns with divergent shapes, which single-loop models could not achieve. The previously proposed threshold mechanism for Wnt3 expression based on {beta}-catenin prepatterns could not explain the data. Our results suggest a more complex patterning mechanism in other animals, where axis and head formation may not be controlled by a single process.

developmental biology↗

bioRxiv2017

Genetic knockdown and knockout approaches in Hydra

Hydra is a member of the Cnidaria, an ancient phylum at the base of metazoan evolution and sister group to all bilaterian animals. The regeneration capacity of Hydra, mediated by its stem cell systems is unparalleled in the animal kingdom. The recent sequencing of the Hydra genome and that of other cnidarians has drawn new attention to this well-known model organism. In spite of this, the establishment of methods to manipulate gene expression in Hydra have remained a major challenge. Here we report a CRISPR-Cas9 based targeted mutation approach as well as an optimized, reproducible strategy for the delivery of siRNAs. Both approaches are based on a refined electroporation protocol for adult Hydra polyps. We demonstrate that these strategies provide reliable genetic interference with target gene expression, facilitating functional studies and genome editing in Hydra.

developmental biology↗