Biology subjects

Izeddin, I.

Publications and source records attributed to Izeddin, I..

6 recordsLinked to original sources

bioRxiv2026

Novel estimation of memory in molecular dynamics with extended and comprehensive single-molecule tracking software: FreeTrace

Single-molecule tracking (SMT) in live cells reveals how biomolecules explore crowded intracellular environments, yet most tracking software assumes Brownian motion, an approximation that fails when anomalous diffusion dominates. This leads to biased trajectory reconstruction and loss of biophysical information, particularly for the short trajectories typical of intracellular experiments. We present FreeTrace, an SMT framework that reconstructs trajectories under fractional Brownian motion (fBm), incorporating temporal correlations directly into linking with minimal input parameters. A deep neural network estimates diffusion properties (Hurst exponent H and generalised diffusion coefficient K) for individual trajectories, while an analytical ensemble estimator accurately recovers H from trajectories as short as three frames, conditions where mean-squared displacement methods fail. Benchmarking on simulated data demonstrates superior performance across motion types and densities. Applications to chromatin-bound histones, DNA repair proteins in S.c. yeast and human cells reveal biologically meaningful diffusion subpopulations, with H values consistent with polymer models and confined motion. FreeTrace bridges theoretical anomalous diffusion models and routine biological experiments.

molecular biology↗

bioRxiv2024

EVE is an open modular data analysis software for event-based localization microscopy

Event-based sensors (EBS), or neuromorphic vision sensors, offer a novel approach to imaging by recording light intensity changes asynchronously, unlike conventional cameras that capture light over fixed exposure times. This capability results in high temporal resolution, reduced data redundancy, and a wide dynamic range. This makes EBS ideal for Single-Molecule Localization Microscopy (SMLM) as SMLM relies on the sequential imaging of sparse, blinking fluorescent emitters to achieve super-resolution. Recent studies have shown that EBS can effectively capture these emitters, achieving spatial resolution comparable to traditional cameras. However, existing analyses of event-based SMLM (eveSMLM) data have relied on converting event lists into image frames for conventional analysis, limiting the full potential of the technology. To overcome this limitation, we developed EVE, a specialized software for analyzing eveSMLM data. EVE offers an integrated platform for detection, localization, and post-processing, with various algorithmic options tailored for the unique structure of eveSMLM data. EVE is user-friendly and features an open, modular infrastructure that supports ongoing development and optimization. EVE is the first dedicated tool for event-based SMLM, transforming the analysis process to fully utilize the spatiotemporal data generated by EBS. This allows researchers to explore the full potential of eveSMLM and encourages the development of new analytical methods and experimental improvements.

biophysics↗

bioRxiv2023

3D single-molecule super-resolution imaging of microfabricated fractal substrates for cell culture and self-referenced imaging

Microstructures arrayed over a substrate have shown increasing interest due to their ability to provide advanced 3D cellular models, which open new possibilities for cell culture, proliferation, and differentiation. Still, the mechanisms by which physical cues impact the cell phenotype are not fully understood, hence the necessity to interrogate cell behavior at the highest resolution. However, cell 3D high-resolution optical imaging on such microstructured substrates remains challenging due to their complexity, as well as axial calibration issues. In this work, we address this issue by leveraging the self-referenced characteristics of fractal-like structures, which simultaneously modulate cell growth and serve as axial calibration tools. To this end, we use multiscale 3D SiO2 substrates consisting of spatially arrayed octahedral features of a few micrometers to hundreds of nanometers. Through optimizations of both the structures and optical imaging conditions, we demonstrate the potential of these 3D multiscale structures as calibration tools for 3D super-resolution microscopy. We use their intrinsic multiscale and self-referenced nature to simultaneously perform lateral and axial calibrations in 3D single-molecule localization microscopy (SMLM) and assess imaging resolutions. We then utilize these substrates as a platform for high-resolution bioimaging. As proof of concept, we cultivate human mesenchymal stem cells on these substrates, revealing very different growth patterns compared to flat glass. Specifically, the spatial distribution of cytoskeleton proteins is vastly modified, as we demonstrate with 3D SMLM assessment.

biophysics↗

bioRxiv2022

Label-free virus-antibody interaction monitoring in real-time by common-path interferometry

Viruses can affect all life forms, raising concerns about virus detection and quantification of small nanoparticles. In this paper we use a label-free, full-field, incoherently illuminated common path interferometric method to detect, track, and quantify biotic nanoparticles. The detection consists of amplifying the light scattered by single nanoparticles in the sample solution. Then, the use of single-particle tracking analysis is used to monitor the change in particle diffusive mobility. With this approach, the recognition signature of T5 phages with purified antibodies targeting the major capsid protein is detected in a few minutes. We also tracked the interaction between SPP1 phages and physiological non-purified serum-containing multiples antibodies molecules. The first interactions occur after around one minute, and the recognition signature is detectable after minutes. In addition, we have been able to differentiate two populations of similar size of empty and full (encapsulating DNA) capsids of T5 in a heterogeneous solution demonstrating the robustness of this label-free detection approach. Furthermore, by combining the diffusion coefficient to the number of tracked particles, we were able to estimate the affinity of the virus-antibodies reaction.

biophysics↗

bioRxiv2022

Event-based vision sensor enables fast and dense single-molecule localization microscopy

Single-molecule localization microscopy (SMLM) is often hampered by the fixed frame rate of the acquisition. Here, we present an alternative new approach to data acquisition and processing based on an affordable event-based sensor. This type of sensor reacts to light intensity changes rather than integrating photons during each frame exposure time. This makes it particularly suited to SMLM, where the ability to surpass the diffraction-limited resolution is provided by blinking events. Each pixel works independently and returns a signal only when an intensity change is detected. Since the output is a list containing only useful data rather than a series of frames, the temporal resolution is significantly better than typical scientific cameras. We demonstrate event-based SMLM super-resolution imaging on biological samples with spatial resolution on par with EMCCD or sCMOS performance. Furthermore, taking advantage of its unique properties, we use event-based SMLM to perform very dense single-molecule imaging, where framebased cameras experience significant limitations.

biophysics↗

bioRxiv2021

Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability

Centromeric regions of human chromosomes contain large numbers of tandemly repeated -satellite sequences. These sequences are covered with constitutive heterochromatin which is enriched in trimethylation of histone H3 on lysine 9 (H3K9me3). Although well studied using artificial chromosomes and global perturbations, the contribution of this epigenetic mark to chromatin structure and genome stability remains poorly known in a more natural context. Using transcriptional activator-like effectors (TALEs) fused to a histone lysine demethylase (JMJD2B), we were able to reduce the level of H3K9me3 on the -satellites repeats of human chromosome 7. We show that the removal of H3K9me3 affects chromatin structure by increasing the accessibility of DNA repeats to the TALE protein. Tethering TALE-demethylase to centromeric repeats impairs the recruitment of HP1 and proteins of Chromosomal Passenger Complex (CPC) on this specific centromere. Finally, the epigenetic re-writing by the TALE-JMJD2B affects specifically the stability of chromosome 7 upon mitosis, highlighting the importance of H3K9me3 in centromere integrity and chromosome stability, mediated by the recruitment of HP1 and the CPC.

molecular biology↗