Biology subjects

Aryal, U.

Publications and source records attributed to Aryal, U..

8 recordsLinked to original sources

bioRxiv2026

Shaping hydrogel bioinks into 3D, multiscale, perfusable models using multimodal printing

Despite technological advances, the fabrication of multiscale, multi-material, and topologically complex 3D structures using soft hydrogel bioinks remains a challenge due to the inherent trade-offs between print size/resolution, bioink properties, and design complexity. In this work, we combine additive (macroscale) digital light projection (DLP) mode with subtractive (microscale) two-photon ablation (TPA) mode with multi-material exchange capability. We identify ideal hydrogel bioink formulations that are compatible with both DLP and TPA modes of processing. Technical challenges related to multimodal fabrication such as alignment of multiscale topologies to facilitate seamless media perfusion, soft-hard multi-material printing to facilitate handling of mechanically weak hydrogel constructs, and hydrogel swelling during printing, were resolved. To highlight the novelty of this hybrid platform, we fabricated centimeter-scale bioink constructs with embedded microscale perfusable topologies that cannot be achieved by isolated use of either DLP or TPA modes. This includes simpler microfluidic chips with independently perfusable microchannels to more complex 3D constructs with embedded, multiscale, perfusable dual-fluidic circuits that mimic the alveoli-capillary interface, or microfluidic chips with endothelialized microchannels. The unique ability of this multimodal platform to mimic in vivo-like multiscale complexities can be potentially used to develop next-generation organ-on-chips.

bioengineering↗

bioRxiv2026

Artificial capillaries-on-a-chip with modular control over lumen size, architecture, in situ modifications and co-culture conditions.

Currently in vitro models of microvascular biology rely on self-assembly of vascular cells in compatible gels. However, the stochastic nature of this process results in large variations in lumen sizes, perfusion continuity, and shear stresses making systematic and reproducible analysis challenging. Here, we report a new technology to generate artificial capillaries on a chip with custom control over lumen sizes and architectures using a combination of femtosecond laser cavitation and collagen casting within multi-chambered microfluidic chips. The design allows seeding of endothelial cells within capillary-sized microchannels and seeding of stromal cells within top-open silos, with independent control over seeding sequence and media compositions. Results show that endothelialized microchannels, coined as artificial capillaries, exhibit excellent barrier function with reproducible control over lumen sizes ({phi}=8-35{micro}m) and their architectures (straight, curvatures, tapered, branched). The physical flow parameters measured across the lumen (namely, flow shear) and at the channel outlets (flow velocities) have been validated against high-fidelity numerical assessments from the Large Eddy Simulation scheme within the digitized versions of the microchannels. The experiment-computation compatibility enabled us to predict changes in regional velocity and wall shear stresses within artificial capillaries, for various capillary architectures. We also show that in situ editing of artificial capillaries in the form of adding new branches or adding occlusions is possible. Lastly, we developed a co-culture model which enables the study of stromal cells with artificial capillaries using conventional imaging methods. We envision that acellular chips with two seeding ports can be readily shipped worldwide and could potentially be adopted as a new technology to study microvascular biology in a reproducible manner.

bioengineering↗

bioRxiv2026

Severity-dependent proteomic alterations in the rat hippocampus following pilocarpine-induced status epilepticus

Status epilepticus (SE) is a prolonged seizure state that can induce lasting hippocampal damage and promote the development of spontaneous seizures and cognitive deficits. The severity and duration of SE strongly influence these long-term outcomes; however, many experimental studies rely on behavioral assessments such as the Racine scale, which may not capture subclinical or non-convulsive seizure activity. Consequently, the molecular consequences of lower-severity seizures that do not meet conventional criteria for severe SE, but may nonetheless contribute to epileptogenesis, remain poorly understood. To address this gap, we investigated whether behavioral seizure severity in the pilocarpine model correlates with distinct proteomic alterations in the hippocampus. Seizures were induced in adult male rats using pilocarpine, and animals were behaviorally classified into three groups: control, mild SE, and severe SE. Hippocampal tissue was collected from control (n = 3), mild SE (n = 5), and severe SE (n = 6) rats and subjected to mass spectrometry-based proteomic analysis. Proteomic profiles were analyzed using partial least squares discriminant analysis (PLS-DA), and differentially expressed proteins (DEPs) were identified using volcano plots. Functional enrichment analyses were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases. Our findings revealed distinct hippocampal proteomic signatures across control, mild SE, and severe SE groups, as revealed by PLS-DA. Severe SE was associated with widespread proteomic alterations, including 129 DEPs linked to synaptic structure, RNA regulation, and metabolic processes. In contrast, mild SE was associated with fewer changes (81 DEPs), primarily involving synaptic organization and endocytosis. A direct comparison of the severe and mild SE groups identified 76 DEPs enriched in pathways related to synaptic plasticity and neurodegeneration. Notably, 23 proteins showed a stepwise expression pattern across groups, suggesting a molecular gradient correlated with seizure severity. Correlation analyses identified and further confirmed glial and inflammatory molecules as candidate molecular markers associated with seizure burden. In conclusion, behavioral seizure severity in the pilocarpine model corresponds to distinct hippocampal proteomic profiles, with severe SE inducing broader and more pronounced molecular alterations than mild SE. Importantly, lower-severity SE is associated with biologically meaningful changes in pathways related to synaptic organization and cellular processing, highlighting mechanistic differences between mild and severe SE that may contribute to epileptogenic progression.

neuroscience↗

bioRxiv2024

CELLNET technology: Spatially organized, functional 3D networks at single cell resolution

Cells possess the remarkable ability to generate tissue-specific 3D interconnected networks and respond to a wide range of stimuli. Understanding the link between the spatial arrangement of individual cells and their networks emergent properties is necessary for the discovery of both fundamental biology as well as applied therapeutics. However, current methods spanning from lithography to 3D photo-patterning to acoustofluidic devices are unable to generate interconnected and organized single cell 3D networks within native extracellular matrix (ECM). To address this challenge, we report a novel technology coined as CELLNET. This involves the generation of crosslinked collagen within multi-chambered microfluidic devices followed by femtosecond laser ablation of 3D microchannel networks and cell seeding. Using model cells, we show that cell migrate within ablated networks within hours, self-organize and form viable, interconnected, 3D networks in custom architectures such as square grid, concentric circle, parallel lines, and spiral patterns. Heterotypic CELLNETs can also be generated by seeding multiple cell types in side-chambers of the devices. The functionality of cell networks can be studied by monitoring the real-time calcium signaling response of individual cells and signal propagation within CELLNETs when subjected to flow stimulus alone or a sequential combination of flow and biochemical stimuli. Furthermore, user-defined disrupted CELLNETs can be generated by lethally injuring target cells within the 3D network and analyzing the changes in their signaling dynamics. As compared to the current self-assembly based methods that exhibit high variability and poor reproducibility, CELLNETs can generate organized 3D single-cell networks and their real-time signaling responses to a range of stimuli can be accurately captured using simple cell seeding and easy-to-handle microfluidic devices. CELLNET, a new technology agnostic of cell types, ECM formulations, 3D cell-connectivity designs, or location and timing of network disruptions, could pave the way to address a range of fundamental and applied bioscience applications. TeaserNew technology to generate 3D single cell interconnected and disrupted networks within natural extracellular matrix in custom configurations.

bioengineering↗

bioRxiv2023

Droplet bioprinting of acellular and cell-laden structures at high-resolutions

Advances in Digital Light Processing (DLP) based (bio) printers have made printing of intricate structures at high resolution possible using a wide range of photosensitive bioinks. A typical setup of a DLP bioprinter includes a vat or reservoir filled with liquid bioink, which presents challenges in terms of cost associated with bioink synthesis, high waste, and gravity-induced cell settling, contaminations, or variation in bioink viscosity during the printing process. Here, we report a vat-free, low-volume, waste-free droplet bioprinting method capable of rapidly printing 3D soft structures at high resolution using model bioinks. A multiphase many-body dissipative particle dynamics (mDPD) model was developed to simulate the dynamic process of droplet-based DLP printing and elucidate the roles of surface wettability and bioink viscosity. Process variables such as light intensity, photo-initiator concentration, and bioink formulations were optimized to print 3D soft structures ([~]0.4 to 3 kPa) with an XY resolution of 38 {+/-} 1.5 m and Z resolution of 237{+/-}5.4 m. To demonstrate its versatility, droplet bioprinting was used to print a range of acellular 3D structures such as a lattice cube, a Mayan pyramid, a heart-shaped structure, and a microfluidic chip with endothelialized channels. Droplet bioprinting, performed using model C3H/10T1/2 cells, exhibited high viability (90%) and cell spreading. Additionally, microfluidic devices with internal channel network lined with endothelial cells showed robust monolayer formation while osteoblast-laden constructs showed mineral deposition upon osteogenic induction. Overall, droplet bioprinting could be a low-cost, no-waste, easy-to-use, method to make customized bioprinted constructs for a range of biomedical applications.

bioengineering↗

bioRxiv2023

Meniscus-enabled Projection Stereolithography (MAPS)

Light-based additive manufacturing methods have been widely used to print high-resolution 3D structures for applications in tissue engineering, soft robotics, photonics, and microfluidics, among others. Despite this progress, multi-material printing with these methods remains challenging due to constraints associated with hardware modifications, control systems, cross-contaminations, waste, and resin properties. Here, we report a new printing platform coined Meniscus-enabled Projection Stereolithography (MAPS), a vat-free method that relies on generating and maintaining a resin meniscus between a crosslinked structure and bottom window and to print lateral, vertical, discrete, or gradient multi-material 3D structures with little-to-no cross-contamination or waste. We also show that MAPS is compatible with a wide range of resins and can print complex multi-material 3D structures without requiring specialized hardware, software, or complex washing protocols. MAPSs ability to print structures with microscale variations in mechanical stiffness, opacity, surface energy, cell densities, and magnetic properties provides a generic method to make advanced materials for a broad range of applications.

bioengineering↗

bioRxiv2023

Printing double network tough hydrogels using Temperature-Controlled Projection Stereolithography (TOPS)

We report a new method to shape double-network (DN) hydrogels into customized microscale 3D structures that exhibit superior mechanical properties in both tension and compression. A one-pot prepolymer formulation containing photo-cross-linkable acrylamide and thermo-reversible sol-gel {kappa}-carrageenan with a suitable crosslinker, and photo-initiator/absorbers are optimized. A new TOPS system is utilized to photo-polymerize the primary acrylamide network into a 3D structure above the sol-gel transition of {kappa}-carrageenan (80{degrees}C), while cooling down generates the secondary physical {kappa}-carrageenan network to realize tough DN hydrogel structures. 3D structures, printed with high lateral (37m) and vertical (180m) resolutions and superior 3D design freedoms (internal voids), exhibit ultimate stress and strain of 200 kPa and 2400% respectively under tension, and simultaneously exhibit high compression stress of 15 MPa with a strain of 95%, both with high recovery rates. The roles of swelling, necking, self-healing, cyclic loading, dehydration, and rehydration on the mechanical properties of printed structures are also investigated. To demonstrate the potential of this technology to make mechanically reconfigurable flexible devices, we print an axicon lens and show that a Bessel beam can be dynamically tuned via user-defined tensile stretching of the device. This technique can be broadly applied to other hydrogels to make novel smart multifunctional devices for a range of applications.

bioengineering↗

bioRxiv2022

Vimentin supports directional cell migration by controlling focal adhesions

Persistent cell migration requires focal adhesions to assemble and disassemble locally while maintaining global front-rear alignment. The mechanism that enforces this long-range spatial coherence remains unresolved. Here we identify the intermediate filament protein vimentin as a cell-scale organizer that stabilizes focal adhesion alignment during directed fibroblast migration. Using quantitative live-cell imaging, we show that vimentin-deficient fibroblasts lose directional persistence and a complete collapse of global focal adhesion alignment. Quantitative analysis reveals that vimentin stabilizes focal adhesion alignment by constraining angular fluctuations and preserving the periodic bias of adhesion birth across the adhesion field. Loss of vimentin results in smaller, rapidly turning-over adhesions with disrupted orientation. Trajectory analysis reveals a mechanically anchored adhesion state selectively associated with vimentin recruitment, distinguishing mechanical stabilization from biochemical maturation. Super-resolution and iPALM imaging further show that vimentin integrates within the focal adhesion nanoarchitecture near the force-transduction layer. Together, our findings establish that vimentin intermediate filaments impose spatial coherence on adhesion dynamics, converting locally stochastic adhesion assembly, turnover, and disassembly into globally coordinated adhesions and persistent directional migration.

cell biology↗