Biology subjects

Cognet, L.

Publications and source records attributed to Cognet, L..

7 recordsLinked to original sources

bioRxiv2026

Nanoscale rheological heterogeneity revealed by Single Particle orientation Tracking (SPoT) of ultrashort carbon nanotubes in brain tissue

Transport in complex biological tissues is governed by local rheological heterogeneity at the nanoscale, yet probing such environments deep inside living systems remains challenging. Here, we introduce an orientation-sensitive single-particle tracking (SPoT) approach that simultaneously resolves translational and rotational dynamics of individual carbon nanotubes deep within biological tissue. By exploiting the intrinsic dipole-like emission and short-wave infrared luminescence of carbon nanotubes enhanced through the incorporation of quantum color-centers our method enables long-duration tracking with high signal-to-noise ratio in optically dense environments. Crucially, the length of these nanotubes can be precisely shortened down to a few tens of nanometers to adapt to diffusion environmental dimensions, further optimizing the tracking applicability. SPoT of single carbon nanotubes provides access to relative changes in local viscosity, steric constraints, and environmental anisotropy. When applied to the brain extracellular space, SPoT demonstrates that local variations in the translational and rotational diffusion of tracers are heterogeneous and not systematically correlated. By combining trajectory-based signatures of confinement with rotational dynamics, this analysis allows the local contributions of effective viscosity and spatial tortuosity to be disentangled. By enabling combined translational and rotational tracking of nano-emitters over unprecedented depths and timescales, this work establishes a new framework for probing nanoscale transport and rheological heterogeneity in intact biological tissues and more generally in complex diffusive environments.

biophysics↗

bioRxiv2026

Back-illumination Phase Imaging Enables Nanoscale Drift Stabilization in Non-transparent Biological Tissues

High-resolution optical microscopy enables nanoscale investigation of molecular structures but is challenged by sample drift during long acquisitions, particularly in thick biological tissues where trans-illumination is unpractical. Precise stabilization at the nanoscale is critical for high-resolution imaging techniques like localization microscopy and single particle tracking. Here we introduce a method combining homogenized differential phase contrast imaging with cross-correlation-based analysis to achieve automated, precise 3D drift correction applicable under oblique back-illumination. We demonstrate its effectiveness in fixed and live organotypic brain slices, maintaining focus within tens of nanometers and enabling high-quality nanoscale mapping of extracellular structures based on single particle tracking. Furthermore, we illustrate its application to opaque liver tissues combined with near-infrared single particle tracking. Our label-free approach provides a versatile solution for stabilizing optical microscopes in thick non-transparent tissues, facilitating extended high-resolution imaging across increasingly complex biological samples.

biophysics↗

bioRxiv2025

Decoding Amyloid Plaque Penetrability: Exploring Extracellular Space and Rheology2in Plaque-rich Cortex

A hallmark of Alzheimers disease (AD) is the accumulation of amyloid plaques, primarily composed of misfolded amyloid {beta} (A{beta}) peptides. We employed complementary high-resolution imaging techniques to investigate the plaque penetrability and the extracellular space (ECS) rheology in a mouse model of AD. Two-photon shadow imaging in vivo confirmed that a dense ring of cells surrounds cortical amyloid plaques but highlighted the diffusional penetrability of the amyloid core. Quantum dot tracking unveiled that ECS diffusional parameters are heterogeneous in and around plaques, with an elevated diffusivity within and around plaques compared to WT-tissue. The amyloid core showed low nanoparticle density, varying by plaque phenotype. Carbon nanotube tracking confirmed these altered local rheological properties at the level of the whole cortex of AD mice. Finally, we found the extracellular matrix to be dysregulated within the amyloid plaque, which may account for the observed alterations in diffusivity. Our study provides fresh insights for understanding A{beta} plaque penetration, a prerequisite for therapeutic development.

neuroscience↗

bioRxiv2025

Self-Assembled siRNA-Gold Supraclusters Detected at the Single-Molecule Level in the NIR-II Window

Gold nanoclusters (AuNCs) possess unique photophysical properties that make them excellent candidates for advanced bioimaging and single-particle detection. In this work, we report the self-assembly of highly emissive, positively charged NIR-II AuNCs stabilized by cysteamine, directed by small interfering RNA (siRNA), which serves as both a structural and electrostatic modulator. The resulting supramolecular assemblies exhibit quasi-spherical morphologies around 100 nm in diameter, with outstanding colloidal stability, photostability, and enzymatic resistance. Their strong photoluminescence, extending up to 1400 nm, enables robust single- particle detection in solution. Spectroscopic and structural analyses--including fluorescence spectroscopy, small-angle X-ray scattering (SAXS), and single-particle tracking--highlight the pivotal role of siRNA in tuning the assembly process via charge balance and concentration- dependent interactions. Beyond providing insights into the structural and photophysical behavior of nucleic acid-guided AuNC assemblies, these results underscore their promise as multifunctional nanoplatforms for integrated imaging and gene-silencing therapies in biophotonic and theranostic applications.

bioengineering↗

bioRxiv2024

Identification of early-stage liver fibrosis by modifications in the interstitial space diffusive microenvironment using fluorescent single-walled carbon nanotubes

During liver fibrosis, recurrent hepatic injuries lead to accumulation of collagen and other extracellular matrix components in the interstitial space, ultimately disrupting liver functions. Early stages of liver fibrosis may be reversible, but opportunities for diagnosis at these stages are currently limited. Here, we show that the alterations of the interstitial space associated with fibrosis can be probed by tracking individual fluorescent single-walled carbon nanotubes (SWCNTs) diffusing in that space. In a mouse model of early liver fibrosis, we find that nanotubes generally explore elongated areas, whose length decrease as the disease progresses even in regions where histopathological examination does not reveal fibrosis yet. Furthermore, this decrease in nanotube mobility is a purely geometrical effect, as the instantaneous nanotube diffusivity stays unmodified. This work establishes the promise of SWCNTs both for the diagnosis of liver fibrosis at an early stage, and for more in-depth studies of the biophysical effects of the disease.

cancer biology↗

bioRxiv2021

Near-infrared carbon nanotube tracking reveals the nanoscale extracellular space around synapses

We provide evidence of a local synaptic nano-environment in the brain extracellular space (ECS) lying within 500 nm of postsynaptic densities. To reveal this brain compartment, we developed a correlative imaging approach dedicated to thick brain tissue based on single-particle tracking of individual fluorescent single wall carbon nanotubes (SWCNTs) in living samples and on speckle-based HiLo microscopy of synaptic labels. We show that the extracellular space around synapses bears specific properties in terms of morphology at the nanoscale and inner diffusivity. We finally show that the ECS juxta-synaptic region changes its diffusion parameters in response to neuronal activity, indicating that this nano-environment might play a role in the regulation of brain activity.

biophysics↗

bioRxiv2019

Fluorescent Sp3 Defect-Tailored Carbon Nanotubes Enable NIR-II Single Particle Imaging in Live Brain Slices at Ultra-Low Excitation Doses

Cellular and tissue imaging in the second near-infrared window (NIR-II, [~]1000 - 1350 nm) is advantageous for in vivo studies because of low light extinction by biological constituents at these wavelengths. However, deep tissue imaging at the single molecule sensitivity has not been achieved in the NIR-II window due to lack of suitable bio-probes. Single-walled carbon nanotubes have emerged as promising near-infrared luminescent molecular bio-probes; yet, their inefficient photoluminescence (quantum yield [~]1%) drives requirements for sizeable excitation doses ([~]1-10 kW/cm2) that are significantly blue-shifted from the NIR-II region (<850 nm) and may thus ultimately compromise live tissue. Here, we show that single nanotube imaging can be achieved in live brain tissue using ultralow excitation doses ([~]100 W/cm2), an order of magnitude lower than those currently used. To accomplish this, we synthesized fluorescent sp3-defect tailored (6,5) carbon nanotubes which, when excited at their first order excitonic transition fluoresce brightly at [~]1160 nm. The biocompatibility of these functionalized nanotubes, which are wrapped by state-of-the-art encapsulation agents (phospholipid-polyethylene glycol), is demonstrated using standard cytotoxicity assays. Single molecule photophysical studies of these biocompatible nanotubes allowed us to identify the optimal luminescence properties in the context of biological imaging.

biophysics↗