Biology subjects

Saif, M. T. A.

Publications and source records attributed to Saif, M. T. A..

13 recordsLinked to original sources

bioRxiv2026

CAF contractility controls collagen stiffness through history-dependent competition between mechanical and proteolytic remodeling

Mechanical remodeling by cancer-associated fibroblasts (CAFs) stiffens tumors and can restrict molecular transport, yet the time-resolved coupling between cellular force and matrix mechanical state is poorly defined. Here we use a microfabricated force sensor integrated with 3D CAF-collagen tissue to measure CAF-generated force and collagen stiffness continuously during pharmacological perturbation. ROCK or non-muscle myosin II inhibition reduced force and remarkably drove collagen stiffness below its initial value rather than merely arresting stiffening. This softening was prevented by broad-spectrum MMP inhibition, but only modestly altered by lysyl oxidase inhibition, supporting a competition between force-driven collagen compaction and proteolytic remodeling. Second-harmonic generation imaging showed shorter, thinner and less aligned fibers after ROCK inhibition, while fluorescence recovery after photobleaching indicated faster dextran transport. Moreover, CAF contractile adaptation depended strongly on the duration of inhibition, with reversible recovery after brief treatment, a hyper-contractile rebound following prolonged treatment and washout, and partial force recovery during continuous exposure. These findings identify CAF-matrix mechanics as a dynamic, treatment-history-dependent balance and provide a framework for designing stromal interventions that alter stiffness and transport.

bioengineering↗

bioRxiv2026

Exercise engages a mechanically activated astrocyte state linking muscle activity to hippocampal plasticity

Physical exercise promotes brain health in part through muscle-derived factors that enter the brain, but how peripheral signals are translated into neural responses remain unclear. Here, we identify astrocyte contraction as a previously unrecognized physiological response to exercise signals that may contribute to adult hippocampal neurogenesis. In vivo, voluntary running rapidly induced nuclear localization of the mechanically sensitive transcriptional regulator Yes-associated protein (YAP), and increased non-muscle myosin II phosphorylation in hilar astrocytes in mice, consistent with acute contraction. Using an in vitro platform with ultrasensitive force sensors, we found that factors released by contracting skeletal muscles activated astrocytes which in turn increased contraction that was necessary and sufficient for their proliferation and expansion. Activated astrocytes subsequently released soluble factors that modulated neuronal network tension and promoted immature neuron abundance. These findings identify astrocyte contractility as a physiological transducer of exercise-derived muscle signals and establish cellular force generation as a potential mechanism regulating neuroplasticity.

neuroscience↗

bioRxiv2026

Opposing mechanical anchorage drives collective cell-matrix interaction

Collective cell behaviors emerge from mechanical interactions with the extracellular matrix (ECM), yet the physical principles governing long-range cell-cell communication remain elusive. Existing models assume that neighboring cells couple by strain-stiffening the ECM between them, amplifying contractility through positive feedback. Here we show that pairwise interactions are insufficient. Instead, stable mechanical communication requires opposing mechanical anchors that allow a cell to strain-stiffen the matrix on both sides. Combining ECM strain mapping, direct cell-force measurements, and live-cell imaging, we find that isolated cell pairs generate only weak, stochastic matrix strains without persistent interactions. In contrast, cells supported by opposing neighbors, or rigid beads acting as mechanical anchors, generate large bilateral matrix strains, increase effective matrix stiffness, align collagen fibers, and form stable multicellular networks. To explain these observations, we develop a predictive mechanosensitive theory introducing effective matrix stiffness and a critical contractile force governing the transition from stochastic to persistent interaction. The theory predicts, and experiments confirm, that opposing mechanical anchorage enables cells to exceed the critical force, trigger collective matrix remodeling, and compact the matrix through collagen-fiber buckling. Together, these findings provide a unifying framework for understanding collective force generation in development, wound repair, fibrosis, and tumor progression.

biophysics↗

bioRxiv2025

Living Neurosheets: Engineering readily deployable neural architectures

Inspired by the ability of brain structures to support cognitive processing, the need for reliable queryable neural models, and emerging biohybrid applications, we present Living Neurosheets: practical, malleable, modular, and scalable systems for realizing living neural architectures, bio-inspired or beyond evolutionary precedent. By innervating porous sheets, paper-like substrates are endowed with neural function while retaining exceptional versatility. Pre-programmed porosity anchors deposited neurons for reliable spatial control. Cutting, folding, and stacking allow intuitive design, modular composition, and batch fabrication (by the hundreds) of complex neural motifs that preserve geometry and function for months. Reversible integration with tissue-matched optoelectronics enables both sample reuse across hardware and hardware multiplexing across samples, for high-throughput, multimodal investigations. We illustrate these aspects across tissue topologies, gyri-inspired manifolds, and laminar cortical mimics, attaining control over entrainment, synchronization, propagation, suppression, and augmentation dynamics--key features of in vivo neural activity. Finally, via cross-instrument portability, we fuse spatial transcriptomics and electrophysiology, linking gene programs to emergent dynamics.

neuroscience↗

bioRxiv2025

Biomechanical 3D tumor models on a micro-milled high-throughput force sensor array

The tumor microenvironment plays a critical role in drug resistance, with extracellular matrix (ECM) mechanics, cell-cell crosstalk, and transport barriers contributing to poor therapeutic outcomes. Traditional two-dimensional (2D) cultures fail to capture these features, and drug efficacy in 2D often does not translate to three-dimensional (3D) models or in vivo tumors. Here, we introduce a 3D tumor model integrated with a high- throughput biomechanical sensor array that enables simultaneous measurement of cellular forces, matrix remodeling, and molecular transport. Fabricated using a scalable and cost-effective micro-milling approach, the platform allows parallel generation of multiple tumor constructs within a single dish. Using patient-derived pancreatic ductal adenocarcinoma (PDA) cells and stromal fibroblasts, we show that responses to gemcitabine and all-trans retinoic acid (ATRA) in 3D differ markedly from 2D cultures, consistent with clinical observations. By integrating biochemical and biomechanical readouts, this technology provides a more physiologically relevant tumor model and a powerful tool for preclinical drug testing and personalized medicine.

cancer biology↗

bioRxiv2024

A fast, muscle-actuated biohybrid swimming robot

The integration of biological actuators with soft scaffolds has led to biohybrid robots including microscale flagellate-like swimmers which generate thrust by waving their flagella-like tails. However, they achieve swimming speeds of only 0.014 body lengths per minute, Reynolds number (Re) [~] 10-3, which is much slower than natural flagellates (O(102 - 103) body lengths per minute). To investigate this, we applied theoretical and experimental methods, including fabrication of a swimmer that converts muscle contractions into large angular tail displacements, reaching swimming speeds of 86.8 m/s (0.58 body lengths per minute), surpassing low-Re predictions. Swimming dynamics sharply transition from a low-Re ([~] 10-3) to an intermediate-Re ([~] 0.1) regime when the actuation angle exceeded 4{degrees}. We used the swimmer to study the ability of muscle to adapt to mechanical stiffness and the beneficial effects of neuromuscular coculture on muscle development. These insights into mechanical and chemical cues will help optimize future biobots. TeaserHow are biological flagellate swimmers like E. coli and sperm cells so fast? We have built a new biohybrid robot to explore the theory.

bioengineering↗

bioRxiv2023

`Mind in Vitro' platforms: Versatile, scalable, robust and open solutions to interfacing with living neurons

Motivated by the unexplored potential of in vitro neural systems for computing, and by the corresponding need of versatile, scalable interfaces for multimodal interaction, we present an accurate, modular, fully customizable and portable recording/stimulation solution that can be easily fabricated, robustly operated, and broadly disseminated. A reconfigurable platform that works across multiple industry standards enables a complete signal chain, from neural substrates sampled through high-density Micro-Electrode Arrays (MEAs) to data acquisition, downstream analysis and cloud storage. Built-in modularity supports the seamless integration of electrical/optical stimulation and fluidic interfaces. Custom MEA fabrication leverages maskless photolithography, favoring the rapid prototyping of a variety of configurations and spatial topologies. Through a native analysis and management software suite, the utility and robustness of our system is demonstrated across neural cultures and applications, including embryonic stem cell-derived and primary neurons, organotypic brain slices, 3D engineered tissue mimics, concurrent calcium imaging and long-term recording. Overall, our technology, termed Mind in Vitro to underscore the computing inspiration, provides an end-to-end solution that can be widely deployed due to its affordable (>10X cost-reduction) and open-source nature, catering to the expanding needs of both conventional and unconventional electrophysiology.

neuroscience↗

bioRxiv2023

Synapses without tension fail to fire in an in vitro network of hippocampal neurons.

Neurons in the brain communicate with each other at their synapses. It has long been understood that this communication occurs through biochemical processes. Here, we reveal a previously unrecognized paradigm wherein mechanical tension in neurons is essential for communication. Using in vitro rat hippocampal neurons, we find that (1) neurons become tout/tensed after forming synapses resulting in a contractile neural network, and (2) without this contractility, neurons fail to fire. To measure time evolution of network contractility in 3D (not 2D) extracellular matrix, we developed an ultra-sensitive force sensor with 1 nN resolution. We employed Multi-Electrode Array (MEA) and iGluSnFR, a glutamate sensor, to quantify neuronal firing at the network and at the single synapse scale, respectively. When neuron contractility is relaxed, both techniques show significantly reduced firing. Firing resumes when contractility is restored. Neural contractility may play a crucial role in memory, learning, cognition, and various neuropathologies.

neuroscience↗

bioRxiv2023

Engineering 3D neuronal networks with directional endogenous neuronal plasticity pathways

The forward engineering of the structure and function of three-dimensional millimeter to centimeter scale living Neuronal Tissue Mimics (NTMs) can advance many engineering and biomedical applications. While hydrogels and 3D printing have achieved major breakthroughs in the development of cm-scale neural tissues that mimic structural morphologies in native neural networks, controlling and programming the resulting function of these NTMs have remained elusive. In this work, using human embryonic stem cell derived optogenetic neurons, we report the in-situ formation of the NTMs on a 2-dimensional micro electrode array with an intimate electrical contact between the electrodes and the tissue. These NTMs were optimized during the differentiation phase of the cells to enrich for neuronal populations that expressed receptors responsible for activating spike-timing dependent plasticity (STDP). Using an optical stimulation regiment with millisecond temporal and micrometer spatial resolution, we were able to program the otherwise omnidirectional spontaneous firing in the NTMs to demonstrate directional firing across different shapes of the NTMs. Our work can pave the way for developing cellular based computational devices, bio-processors, and biological memories.

bioengineering↗

bioRxiv2022

Astrocyte-mediated transduction of muscle fiber contractions synchronizes hippocampal neuronal network development

Exercise supports brain health in part through enhancing hippocampal function. The leading hypothesis is that muscles release factors when they contract (e.g., lactate, myokines, growth factors) that enter circulation and reach the brain where they enhance plasticity (e.g., increase neurogenesis and synaptogenesis). However, it remains unknown how the muscle signals are transduced by the hippocampal cells to modulate network activity and synaptic development. Thus, we established an in vitro model in which the media from contracting primary muscle cells (CM) is applied to developing primary hippocampal cell cultures on a microelectrode array. We found that the hippocampal neuronal network matures more rapidly (as indicated by synapse development and synchronous neuronal activity) when exposed to CM than regular media (RM). This was accompanied by a 1.4-fold and 4.4-fold increase in the proliferation of neurons and astrocytes, respectively. Further, experiments established that the astrocytes release factors that inhibit neuronal excitability and facilitate network development. Results provide new insight into how exercise may support hippocampal function through regulating astrocyte proliferation and subsequent taming of neuronal activity into an integrated network. HighlightsO_LIContracting muscle conditioned media enhances neuronal activity. C_LIO_LIContracting muscle conditioned media expedites neuronal maturation and accumulation of filamentous actin at presynaptic terminals. C_LIO_LIContracting muscle conditioned media induces significant neuron and astrocyte proliferation. C_LIO_LIAstrocytes release factors that inhibit muscle media-induced neuronal activity. C_LI

neuroscience↗

bioRxiv2021

Empowering Engineered Muscle in Biohybrid Pump by Extending Connexin 43 Duration with Reduced Graphene Oxides

Engineered skeletal muscle act as therapeutics invaluable to treat injured or diseased muscle and a "living" material essential to assemble biological machinery. For normal development, skeletal myoblasts should express connexin 43, one of the gap junction proteins that promote myoblast fusion and myogenesis, during the early differentiation stage. However, myoblasts cultured in vitro often down-regulate connexin 43 before differentiation, limiting myogenesis and muscle contraction. This study demonstrates that tethering myoblasts with reduced graphene oxide (rGO) slows connexin 43 regression during early differentiation and increases myogenic mRNA synthesis. The whole RNA sequencing also confirms that the rGO on cells increases regulator genes for myogenesis, including troponin, while decreasing negative regulator genes. The resulting myotubes generated a three-fold larger contraction force than the rGO-free myotubes. Accordingly, a valveless biohybrid pump assembled with the rGO-tethered muscle increased the fluid velocity and flow rate considerably. The results of this study would provide an important foundation for developing physiologically relevant muscle and powering up biomachines that will be used for various bioscience studies and unexplored applications.

bioengineering↗

bioRxiv2020

A novel method for sensor-based quantification of single/multi-cellular traction dynamics and remodeling in 3D matrices

Cells in vivo generate mechanical forces (traction) on surrounding 3D extra cellular matrix (ECM) and cells. Such traction and biochemical cues may remodel the matrix, e.g. increase stiffness, which in turn influences cell functions and forces. This dynamic reciprocity mediates development and tumorigenesis. Currently, there is no method available to directly quantify single cell traction and matrix remodeling in 3D. Here, we introduce a method to fulfil this long-standing need. We developed a high-resolution microfabricated sensor which hosts a 3D cell-ECM tissue formed by self-assembly. It measures cell forces and tissue-stiffness and can apply mechanical stimulation to the tissue. We measured single and multicellular force dynamics of fibroblasts (3T3), human colon (FET) and lung (A549) cancer cells and cancer associated fibroblasts (CAF05) with 1 nN resolution. Single cells show significant force fluctuations in 3D. FET/CAF co-culture system, mimicking cancer tumor microenvironment, increased tissue stiffness by 3 times within 24 hours.

bioengineering↗

bioRxiv2020

Development of an objective index, neural activity score (NAS), reveals neural network ontogeny and treatment effects on microelectrode arrays

Microelectrode arrays (MEAs) are valuable tools for electrophysiological analysis at a cellular population level, providing assessment of neural network health and development. Analysis can be complex, however, requiring intensive processing of large high-dimensional data sets consisting of many activity parameters. As a result, valuable information is lost, as studies subjectively report relatively few metrics in the interest of simplicity and clarity. From a screening perspective, many groups report simple overall activity; we are more interested in culture health and changes in network connectivity that may not be evident from basic activity parameters. For example, general changes in overall firing rate - the most commonly reported parameter - provide no information on network development or burst character, which could change independently. Our goal was to develop a fast objective process to capture most, if not all, the valuable information gained when using MEAs in neural development and toxicity studies. We implemented principal component analysis (PCA) to reduce the high dimensionality of MEA data. Upon analysis, we found that the first principal component was strongly correlated to time, representing neural culture development; therefore, factor loadings were used to create a single index score - named neural activity score (NAS) - reflective of neural maturation. To validate this score, we applied it to studies analyzing various treatments. In all cases, NAS accurately recapitulated expected results, suggesting this method is viable. This approach may be improved with larger training data sets and can be shared with other researchers using MEAs to analyze complicated treatment effects and multicellular interactions. Author SummaryAnalyzing neural activity has important applications such as basic neuroscience research, understanding neurological diseases, drug development, and toxicity screening. Technology for recording neural activity continues to develop, producing large data sets that provide complex information about neuronal function. One specific technology, microelectrode arrays (MEAs), has recently given researchers the ability to record developing neural networks with potential to provide valuable insight into developmental processes and pathological conditions. However, the complex data generated by these systems can be challenging to analyze objectively and quantitatively, hindering the potential of MEAs, especially for high-throughput approaches, such as drug development and toxicity screening, which require quick, simple, and accurate quantification. Therefore, we have developed an index for simple quantification and evaluation of neural network maturation and the effects of perturbation. We present validation of our approach using several treatments and culture conditions, as well as a meta-analysis of toxicological screening data to compare our approach to current methods. In addition to providing a simple quantification method for neural network activity in various conditions, our method provides potential for improved results interpretation in toxicity screening and drug development.

neuroscience↗