Biology subjects

Grimm, M.

Publications and source records attributed to Grimm, M..

3 recordsLinked to original sources

bioRxiv2024

Toll-like receptor 3 orchestrates a conserved mechanism of heart regeneration

The humans heart responds to tissue damage with persistent fibrotic scarring. Unlike humans, zebrafish can repair cardiac injury and re-grow heart tissue throughout life. Recently, Toll-like receptor 3 (Tlr3) was identified as an important mediator of cardiac regeneration in neonatal mice. However, no functional analysis of tlr3 knock-out mutant zebrafish in respect to cardiac regeneration has yet been performed. We hypothesize that TLR3 signalling plays a central, conserved role in driving cardiac regeneration upon injury. Therefore, we focused on tlr3 mediated cardiac regeneration in zebrafish, ultimately discovering an evolutionary conserved mechanism of heart repair. Using histological, behavioural, and RNA-Sequencing analysis, we uncovered a conserved mechanism of tlr3 mediated cardiac repair after myocardial injury. Upon myocardial cryoinjury subjection, survival is decreased in tlr3-/- fish as compared to wildtype controls. Tlr3-/- zebrafish fail to recruit immune cells to the injured ventricle, resulting in impaired DNA repair and transcriptional reprogramming of cardiomyocytes. Mechanistically, we uncover an evolutionary conserved mechanism of tlr3 activation in fibroblasts promoting monocyte migration towards an injured ventricular area. Our data reveal tlr3 as a novel therapeutic target to promote cardiac regeneration. Every experiment including human participants has been approved by the ethics committee of the Medical University of Innsbruck (Ref. Nr.: 1262/2023). All experiments including the use of laboratory animals have been approved by the federal ministry of education, science, and research of Austria (Ref. Nr.: 2020-0.345.504).

molecular biology↗

bioRxiv2022

Protein-based Virtual Screening Tools applied for RNA-Ligand Docking identify new Binders of the preQ1-Riboswitch

Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programmes to reproduce native binding modes of small molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programmes were found to perform similar compared to the RNA-based docking tool rDOCK and the faced challenges during docking, namely protomer and tautomer selection, target dynamics and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective virtual screening with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID and FlexX, followed by microscale thermophoresis assays identified 6 active compounds out of 23 tested virtual screening hits with potencies between 29.5 nM and 11.0 M. The hits were selected not solely based on their docking score, but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based virtual screenings against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.

bioinformatics↗

bioRxiv2021

Novel piece of the puzzle: ALI1 is required for oxo-C14-HSL priming in Arabidopsis

Quorum sensing (QS) molecules mediate communication between bacterial cells. N-acyl homoserine lactones (AHL) are one of the best-studied groups of QS molecules. In addition to bacterial communication, AHL are involved in interactions with eukaryotes. Short side-chain AHL are readily taken up by plants. They induce root elongation and growth promotion. Hydrophobic long side-chain AHL are usually not transported over long distances although, they may prime plants for enhanced resistance. Unfortunately, studies elucidating the plant factors required for response to AHL are sparse. Here, we provide evidence of a plant protein, namely the AHL-priming protein 1 (ALI1), indispensable for enhanced resistance response induced by the N-3-oxotetradecanoyl-homoserine lactone (oxo-C14-HSL). Comparing Col-0 and the ali1 mutant, we revealed loss of AHL-priming in ali1. This phenomenon is reverted with the reintroduction of ALI1 into ali1. Additional transcriptome analysis revealed that ali1 is less sensitive to oxo-C14-HSL treatment compared to the wild-type. Our results suggest, therefore, that ALI1 is required for oxo-C14-HSL-dependent priming for enhanced resistance in Arabidopsis.

plant biology↗