Biology subjects

Dam, T.

Publications and source records attributed to Dam, T..

3 recordsLinked to original sources

bioRxiv2026

Targeted Epigenetic Modulation Outperforms Nuclease- and Deaminase-Based Editing for Durable Pcsk9 Silencing in a Clinically Relevant Delivery System

Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) lowers low-density lipoprotein cholesterol, a major risk factor for cardiovascular disease. Although several gene therapy strategies targeting Pcsk9 have been developed, direct comparisons across modalities are limited. To address this, we systematically evaluated cytosine base editing, nuclease-based CRISPR-Cas9, and epigenetic gene editing for Pcsk9 suppression. We first engineered a cytosine base editor to introduce a premature stop codon, then optimized and characterized an epigenetic editor, and finally delivered all modalities as mRNA formulated in Arcturus lipid nanoparticles (LUNAR(R)) into wild-type mice, benchmarking them against conventional CRISPR-Cas9 and GalNAc-siRNA. Remarkably, epigenetic editing achieved the most efficient and sustained repression of PCSK9, maintaining low protein levels throughout the entire 30-day study period. By comparison, cytosine base editing reduced PCSK9 with minimal double-stranded DNA breaks and off-target effects, but editing precision requires further improvement, while GalNAc-siRNA produced only transient suppression, limiting its suitability for a one-time therapeutic approach. Collectively, these findings highlight the superior durability and efficacy of epigenetic gene editing and provide proof-of-concept for its combination with LUNAR(R) delivery as a promising strategy for long-lasting hepatic-targeted therapy.

molecular biology↗

bioRxiv2025

A light-weight segmentation method for multi-state Brownian trajectories

Single-particle tracking methods have emerged as a crucial tool for the characterization of dynamical and diffusive processes in a range of biological and synthetic systems. Here, we propose a simple and light-weight yet accurate method for the segmentation of multi-state Brownian trajectories based on an optimised Gaussian filtering of the displacement time series combined with an automated fitting to a Gaussian mixture model. We verify our method using synthetic, 2-state Brownian trajectories and show that our method provides high levels of accuracy in terms of segmentation and the estimation of self-diffusion coefficients for reasonably well-separated values of the diffusion coefficients. We furthermore demonstrate the feasibility of our method on experimental systems using single-particle tracking data for diffusing membrane proteins bound to a supported lipid bilayer. Compared to methods based on deep learning or hidden Markov models our method imposes a much lower computational load, making it suitable for fast and accurate online processing of single-particle trajectories from microscopy images.

biophysics↗

bioRxiv2019

The maize Hairy Sheath Frayed1 (Hsf1) mutant alters leaf patterning through increased cytokinin signaling

Leaf morphogenesis requires growth polarized along three axes - proximal-distal, medial-lateral and abaxial-adaxial. Grass leaves display a prominent proximal-distal (P-D) polarity consisting of a proximal sheath separated from the distal blade by the auricle and ligule. Although proper specification of the four segments is essential for normal morphology, our knowledge is incomplete regarding the mechanisms which influence P-D specification in monocots like maize (Zea mays). Here we report the identification of the gene underlying the semi-dominant, leaf patterning, maize mutant Hairy Sheath Frayed1 (Hsf1). Hsf1 plants produce leaves with outgrowths consisting of proximal segments - sheath, auricle and ligule - emanating from the distal blade margin. Analysis of three independent Hsf1 alleles revealed gain-of-function missense mutations in the ligand binding domain of the maize cytokinin (CK) receptor Zea mays Histidine Kinase1 (ZmHK1) gene. Biochemical analysis and structural modeling suggest the mutated residues near the CK binding pocket affect CK binding affinity. Treatment of wild type seedlings with exogenous CK phenocopied the Hsf1 leaf phenotypes. Results from expression and epistatic analyses indicated the Hsf1 mutant receptor appears to be hypersignaling. Our results demonstrate that hypersignaling of CK in incipient leaf primordia can reprogram developmental patterns in maize.\n\nSummaryIncreased cytokinin signaling in the maize Hairy Sheath Frayed1 mutant modifies leaf development leading to changes in pattering, growth and cell identity.

plant biology↗