Biology subjects

Aramesh, M.

Publications and source records attributed to Aramesh, M..

6 recordsLinked to original sources

bioRxiv2026

Controlling Molecular Transport through Nanopores by Dynamic Aperture Sizing

Molecular transport through a nanopore determines the information that can be recovered from a translocation signal, yet it remains difficult to control in conventional solid-state nanopores. Rapid translocation reduces the information content and fixed nanopore geometries limit the dimensionality of the signal. Here, we control molecular transport through the development of the pipette-elastomer interfacial nanopore (PEIN), a dynamically reconfigurable solid-state nanopore which addresses these limitations. A PEIN is formed by depressing a glass nanopipette into a soft elastomer, progressively constricting its aperture and enabling continuous control over aperture size, while retaining the simplicity and favourable noise characteristics of glass nanopipette sensing. Using the dynamic aperture size control, DNA velocities could be controlled over more than a twofold range, with dwell times two orders of magnitude greater than observed in glass nanopipettes. DNA-origami rulers further revealed a progressive reduction in polymer velocity during translocation, indicating that hydrodynamic drag alone is insufficient to model forces on the DNA polymer. Finally, by using single- and double-stranded DNA and gold nanoparticles as molecular standards, we demonstrate reversible, size-selective molecular gating with sub-nanometre control. These results establish the PEIN as an accessible platform for controlling molecular transport and probing the relationships among biopolymer conformation, nanoscale confinement and translocation dynamics.

biophysics↗

bioRxiv2025

Tuning the Mechanical Properties and Printability of Viscoelastic Skin-Derived Hydrogels for 3D Cell Culture

In vitro investigations or tissue engineering require the creation of hierarchical and acellularized 3D structures mimicking the native environment of cells in vivo. Bioprinting provides a powerful approach to fabricating 3D architectures with precision and control. However, developing a bioink suitable for 3D cell culture remains challenging, particularly in achieving optimal rheological properties, printability and bioactivity necessary for cellular viability, functionality and growth. Here, we developed tissue-derived hydrogels with tunable gelation kinetics and rheological properties. By precisely adjusting the bioinks physical characteristics, we optimized its printability for extrusion-based bioprinting, enabling fast fabrication of structurally stable constructs that support the formation of 3D cellular structures. A robust decellularization protocol was developed to consistently obtain porcine skin-derived dECM (decellularized extracellular matrix) hydrogels with minimal batch-to-batch variation. The influence of dECM concentration (1-5 mg/mL) on the inks viscoelastic properties, printability, gelation kinetics, and cellular response was investigated. Gelation kinetics varied between 7 minutes to several hours, while the storage modulus ranged between 10 to 1000 Pa. Additionally, more concentrated hydrogels led to more homogeneous prints due to their higher viscosity. Fibroblast cells infiltrated the 3D matrix of the softer hydrogels (1 and 2.5 mg/mL), forming an interconnected network. In contrast, migration was significantly restricted in the denser hydrogels (5 mg/mL). Our findings demonstrate the potential of tissue-derived hydrogels with tunable properties for 3D bioprinting applications, enabling fast and reproducible fabrication of dECM environments for cellular studies and tissue engineering, while highlighting the critical balance between mechanical and biological properties in bioink formulation.

bioengineering↗

bioRxiv2023

Nanotopography boosts cellular uptake by inducing macropinocytosis

Efficient cellular uptake of biomolecules, including genetic material, mRNA, proteins, and nanoparticles, requires novel approaches to overcome inherent cellular barriers. This study investigates how nanotopographical cues from nanoporous surfaces impact the uptake efficiency of diverse molecules by cells. The results demonstrate that cellular uptake efficiency increases significantly on nanoporous surfaces compared to flat surfaces. Notably, this process is found to be dependent on the size and morphology of the nanopores, reaching its peak efficacy with blind pores of 400 nm in size. Enhanced genetic transduction on nanoporous surfaces were observed for multiple vectors, including lentiviruses, baculoviruses, and mRNA molecules. The versatile nature of this approach allows co-transfection of cells with multiple mRNA vectors. Moreover, the nanoporous platform was used for efficient and fast manufacturing of CAR-T cells through lentiviral transduction. Furthermore, we pinpoint macropinocytosis as the predominant mechanism driving increased cellular uptake induced by the nanoporous surfaces. The method introduced here for enhancing genetic transduction of cells has applications in immunotherapy research, drug delivery, and cell engineering.

biophysics↗

bioRxiv2023

Viscoelastic Deformability Cytometry: Ultra-high Throughput Platform for Mechanical Phenotyping of Cells in Liquid and Solid Biopsies

Due to the differences in mechanical properties between cancer cells and their benign counterparts, the mechanical characteristics of cells have emerged as a significant feature in diagnosing cancer. Consequently, measuring cell deformability as a means of mechanical phenotyping is promising for both the detection and classification of the disease. However, performing high-throughput single-cell deformability measurements on liquid or solid tissue biopsies remains a significant challenge within a clinical setting. Herein, we introduce an ultra-high throughput viscoelastic-based microfluidic platform to measure the cell mechanical properties at rates of up to 100,000 cells/s. Thanks to the viscoelastic property of the fluid, cells are focused and deformed within the same platform obviating the need for any sheath fluid. We used the presented platform for cell phenotyping in both liquid and solid tumor biopsies, such as identification of malignant lymphocytes in peripheral blood samples and glioblastoma-type cell classification from solid tumor samples. The presented platform has the potential to open new opportunities in the assessment of cancer, enable precise mechanical profiling of rare cells, and facilitate sensitive diagnostic applications.

bioengineering↗

bioRxiv2021

Nanoconfinement of Microvilli Alters Gene Expression and Boosts T cell Activation

T cells sense and respond to their local environment at the nanoscale by forming small actin-rich protrusions, called microvilli, which play critical roles in signaling and antigen recognition, particularly at the interface with the antigen presenting cells. However, the mechanisms by which microvilli contribute to cell signaling and activation is largely unknown. Here, we present a tunable engineered system that promotes microvilli formation and T cell signaling via physical stimuli. We discovered that nanoporous surfaces favored microvilli formation, and markedly altered gene expression in T cells and promoted their activation. Mechanistically, confinement of microvilli inside of nanopores leads to size-dependent sorting of membrane-anchored proteins, specifically segregating CD45 phosphatases and T cell receptors (TCR) from the tip of the protrusions when microvilli are confined in 200 nm pores, but not in 400 nm pores. Consequently, formation of TCR nanoclustered hotspots within 200 nm pores, allows sustained and augmented signaling that prompts T cell activation even in the absence of TCR agonists. The synergistic combination of mechanical and biochemical signals on porous surfaces presents a straightforward strategy to investigate the role of microvilli in T cell signaling as well as to boost T cell activation and expansion for application in the growing field of adoptive immunotherapy.

bioengineering↗

bioRxiv2020

Functionalized bead assay to measure 3-dimensional traction forces during T-cell activation

When T-cells probe their environment for antigens, the bond between the T-cell receptor (TCR) and the peptide-loaded major histocompatibility complex (MHC) is put under tension, thereby influencing the antigen discrimination process. Yet, the quantification of such forces in the context of T-cell signaling is technically challenging. Common approaches such as traction force microscopy (TFM) employ a global readout of the force fields, e.g. by measuring the displacements of hydrogel-embedded marker beads. Recent data, however, indicated that T-cells exert tensile forces locally via TCR-enriched microvilli while scanning the surface of antigen-presenting cells. Here, we developed a traction force microscopy platform, which allows for quantifying the pulls exerted via T-cell microvilli, in both tangential and normal directions, during T-cell activation. For this, we immobilized specific T-cell activating antibodies directly on the marker beads used to read out the hydrogel deformation. Microvilli targeted the functionalized beads, as confirmed by superresolution microscopy of the local actin organization. Moreover, we found that cellular components, such as actin, TCR and CD45 reorganize upon interaction with the beads, such that actin forms a vortex-like ring structure around the beads and TCR is enriched at the bead surface, whereas, CD45 is excluded from bead-microvilli contacts. Significance statementDuring the antigen recognition process, T-cells explore and probe their environment via microvilli, which exert local pushes and pulls at the surface of the antigen presenting cell. It is currently believed that these forces influence or even enable the antigen recognition process. Here, we describe the development of a platform, which allows us to quantify the magnitude and direction of traction forces exerted locally by T cell microvilli. Simultaneous Ca2+ imaging was used to link the measured forces to the overall T cell activation status. Superresolution microscopy resolved the contact sites of bead-microvilli contact at the nanoscale: cells contacted beads via actin vortex-like structures, which excluded the phosphatase CD45 from the contacts.

biophysics↗