Biology subjects

Yeh, Y.-T.

Publications and source records attributed to Yeh, Y.-T..

16 recordsLinked to original sources

bioRxiv2026

Three-Dimensional Fluid-Structure Interaction Reveals Trade-offs Among Oxygen Delivery, Shear, and Washout in Pediatric Roller-Pump Cardiopulmonary Bypass

Objective: To determine how roller speed, tubing occlusion, and hematocrit jointly regulate oxygen delivery, shear, and washout in pediatric roller-pump cardiopulmonary bypass. Methods: A three-dimensional, closed-loop fluid-structure interaction model resolved roller-tube contact, tubing deformation, and blood flow. Forty simulations combined 4 roller speeds (38-95 revolutions per minute), 2 occlusion levels (77% and 83%), and 5 hematocrit levels (15%-50%). Cycle-averaged flow, oxygen delivery, peak shear stress, and viscosity-normalized relative residence time were quantified. Results: Roller compression produced retrograde leakage through the occluded gap, localized peak shear stress exceeding 100 pascals, and adjacent stagnation and recirculation. Flow increased nearly linearly with roller speed and was higher at greater occlusion, with little hematocrit dependence. Higher speed and occlusion increased peak shear stress while reducing relative residence time; higher hematocrit further increased peak shear stress. Similar oxygen delivery could arise from substantially different flow environments: among 10 conditions providing oxygen delivery of approximately 9-12 milliliters per minute, peak shear stress ranged from approximately 25 to 70 pascals. Within conditions satisfying an illustrative minimum oxygen-delivery threshold, lower hematocrit permitted speed and occlusion settings yielding lower peak shear stress and relative residence time. Conclusions: Pediatric roller-pump settings that provide similar oxygen delivery can expose blood to markedly different shear and washout environments. Joint evaluation of these metrics may guide selection of speed, occlusion, and hematocrit to meet a target oxygen delivery while reducing shear and improving washout. Keywords: Cardiopulmonary bypass; roller pump; pediatric cardiac surgery; fluid-structure interaction; shear stress; relative residence time

bioengineering↗

bioRxiv2026

Mapping fibrotic microenvironments: single-cell and spatial profiling of Schistosoma mansoni-induced tissue fibrosis

Schistosoma-induced tissue fibrosis, driven by immune response to trapped schistosome eggs, is the principal cause of pathology and schistosomiasis-related morbidity. While praziquantel effectively clears adult parasites, no therapies exist to target eggs or egg-induced tissue fibrosis. Here, we utilise single-cell spatial transcriptomics to define the high-resolution molecular architecture of the fibrotic niche in Schistosoma mansoni-infected mice at 8 weeks post-infection. Our data reveal that the host executes divergent, organ-specific biological programs: constructing a rigid, concentric fibrotic granuloma for permanent egg sequestration in the liver while building a flexible, discontinuous collagen architecture in the intestine to facilitate egg transit. Spatially resolved cell-cell interaction analysis, unprecedented in schistosome-induced fibrosis, identifies the strongest cellular interactions between macrophages and collagen-producing cells, with TGF-{beta}-dominant ligand-receptor pairs in the hepatic niche and integrin-centered pairs in the intestine. Despite this architectural divergence, we detected a core signature of five ligand-receptor pairs shared across both tissues, suggesting shared signalling interactions that could be leveraged for pan-tissue therapeutics for treating schistosome-induced fibrosis. Together, these findings provide the first high-resolution spatial atlas of schistosomiasis-associated fibrosis and provide a foundational framework for discovering novel drug targets capable of reversing established tissue damage, addressing a critical clinical gap where current therapies fail.

molecular biology↗

bioRxiv2025

A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability

Recent studies have revealed many alternative exons differentially spliced across diverse neuron types in the mammalian brain, but their links to neuronal physiology remain unclear. Here we characterize a deeply conserved microexon E35a in Ank3 encoding ankyrin-G (AnkG), a multifaceted adaptor protein best known as a master organizer of the axon initial segment (AIS) and as a leading genetic risk factor for bipolar disorder. E35a is predominantly skipped in cortical glutamatergic neurons but included in cortical GABAergic neurons and cerebellar neurons, which is dictated by multiple neuronal splicing factors. In E35a-deletion mice we generated, interneurons show increased excitability and somatic Ca2+ activity, without disruption in AIS. Biochemical analyses suggest that E35a inclusion facilitates AnkG interaction with a protein complex involving inositol trisphosphate receptors (InsP3Rs) important for intracellular Ca2+ signaling. Alternative splicing therefore allows AnkG to modulate neuron type-specific excitability in addition to its ubiquitous pan-neuronal role in organizing the AIS.

neuroscience↗

bioRxiv2024

Neutrophils exhibit distinct migration phenotypes that are modulated by transendothelial migration

The extravasation of polymorphonuclear neutrophils (PMNs) is a critical component of the innate immune response that involves transendothelial migration (TEM) and interstitial migration. TEM-mediated interactions between PMNs and vascular endothelial cells (VECs) trigger a cascade of biochemical and mechanobiological signals whose effects on interstitial migration are currently unclear. To address this question, we cultured human VECs on a fibronectin-treated transwell insert to model the endothelium and basement membrane, loaded PMN-like differentiated HL60 (dHL-60) cells in the upper chamber of the insert, and collected the PMNs that crossed the membrane-supported monolayer from the lower chamber. The 3D chemotactic migration of the TEM-conditioned PMNs through collagen matrices was then quantified. Data collected from over 50,000 trajectories showed two distinct migratory phenotypes, i.e., a high-persistence phenotype and a low-persistence phenotype. These phenotypes were conserved across treatment conditions, and their existence was confirmed in human primary PMNs. The high-persistence phenotype was characterized by more straight trajectories and faster migration speeds, whereas the low-persistence one exhibited more frequent sharp turns and loitering periods. A key finding of our study is that TEM induced a phenotypic shift in PMNs from high-persistence migration to low-persistence migration. Changes in the relative proportion of high-persistence and low-persistence populations correlated with GRK2 expression levels. Inhibiting GRK2 hindered the TEM-induced shift in migratory phenotype and impaired the phagocytic function of PMNs. Overall, our study suggests that TEM-mediated GRK2 signaling primes PMNs for a migration phenotype better suited for spatial exploration and inflammation resolution. These observations provide novel insight into the biophysical impacts of TEM that priming PMNs is essential to conduct sentinel functions.

cell biology↗

bioRxiv2024

Uncertainty-Aware Traction Force Microscopy

Traction Force Microscopy (TFM) is a versatile tool to quantify cell-exerted forces by imaging and tracking fiduciary markers embedded in elastic substrates. The computations involved in TFM are ill-conditioned, and data smoothing or regularization is required to avoid overfitting the noise in the tracked substrate displacements. Most TFM calculations depend critically on the heuristic selection of regularization (hyper)parameters affecting the balance between overfitting and smoothing. However, TFM methods rarely estimate or account for measurement errors in substrate deformation to adjust the regularization level accordingly. Moreover, there is a lack of tools to quantify how these errors propagate to the recovered traction stresses. These limitations make it difficult to interpret TFM readouts and hinder comparing different experiments. This manuscript presents an uncertainty-aware TFM technique that estimates the variability in the magnitude and direction of the traction stress vector recovered at each point in space and time of each experiment. In this technique, substrate deformation and its uncertainty are quantified using a non-parametric bootstrap PIV method by resampling the microscopy image pixels (PIV-UQ). This information is passed to a hierarchical Bayesian framework that automatically selects its hyperparameters to perform spatially adaptive regularization conditioned on image quality and propagates the uncertainty to the traction stress readouts (TFM-UQ). We validate the performance of PIV-UQ and TFM-UQ using synthetic datasets with prescribed image quality variations and demonstrate the application of PIV-UQ and TFM-UQ to experimental datasets. These studies show that TFM-UQ locally adapts the level of smoothing, outperforming traditional regularization methods. They also illustrate how uncertainty-aware TFM tools can be used to objectively choose key image analysis parameters like PIV-UQ interrogation window size. We anticipate that these tools will allow for decoupling biological heterogeneity from measurement variability and facilitate automating the analysis of large datasets by parameter-free, input data-based regularization.

biophysics↗

bioRxiv2023

Deep screening of proximal and distal splicing-regulatory elements in a native sequence context

Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is impeded by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically dead CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identified not only known SREs, but also a novel distal intronic splicing enhancer, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.

molecular biology↗

bioRxiv2023

Tunable photoinitiated hydrogel microspheres for direct quantification of cell-generated forces in complex three-dimensional environments

We present a high-throughput method using standard laboratory equipment and microfluidics to produce cellular force microscopy probes with controlled size and elastic modulus. Mechanical forces play crucial roles in cell biology but quantifying these forces in physiologically relevant systems remains challenging due to the complexity of the native cell environment. Polymerized hydrogel microspheres offer great promise for interrogating the mechanics of processes inaccessible to classic force microscopy methods. However, despite significant recent advances, their small size and large surface-to-volume ratio impede the high-yield production of probes with tunable, monodisperse distributions of size and mechanical properties. To overcome these limitations, we use a flow-focusing microfluidic device to generate large quantities of droplets with highly reproducible, adjustable radii. These droplets contain acrylamide gel precursor and the photoinitiator Lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) as a source of free radicals. LAP provides fine control over microsphere polymerization due to its high molar absorptivity at UV wavelengths and moderate water solubility. The polymerized microspheres can be functionalized with different conjugated extracellular matrix proteins and embedded with fluorescent nanobeads to promote cell attachment and track microsphere deformation. As proof of concept, we measure the mechanical forces generated by a monolayer of vascular endothelial cells engulfing functionalized microspheres. Individual nanobead motions are tracked in 3D and analyzed to determine the 3D traction forces within seconds and without the need for solving an ill-posed inverse problem. These results reveal that the cell monolayer collectively exerts strong radial compression and subtle lateral distortions on the encapsulated probe.

biophysics↗

bioRxiv2022

A single dose of intravenous human amniotic membrane-derived mesenchymal stem cells limits transmural infarction, reduces fibrosis size, and improves left ventricular systolic function in the myocardial ischemic/reperfusion model of rats

Despite the advances in coronary reperfusion in acute myocardial infarction (MI), post-MI heart failure is still a large burden of public health. Transmural infarction and extended fibrosis contribute largely to post-MI systolic dysfunction and heart failure, and thus cardioprotective strategies are crucial. Human amniotic membrane-derived mesenchymal stem cells (hAMSCs) have been shown with properties of immunomodulation, anti-inflammation, and low immunogenicity, which make them good candidates for cell therapies. In this study, a myocardial ischemia/reperfusion (I/R) model was established in rats, and hAMSCs were administered via the tail vein during coronary reperfusion. Compared to the control group, the rats receiving hAMSCs during the I/R procedure (hAMSC group) exhibited significantly better left ventricular ejection fractions after MI. Histological examinations of the hearts in hAMSC group showed minimal transmural infarction 4 weeks after the I/R procedure. Compared to the control group, hAMSC group had reduced size of cardiac fibrosis and less thinning of myocardial wall. In conclusion, intravenous hAMSCs limit transmural infarction, reduce fibrosis size, and improve left ventricular systolic function after MI in the animal model.

cell biology↗

bioRxiv2022

Restoration of PITPNA in Type 2 diabetic human islets reverses pancreatic beta-cell dysfunction

Defects in insulin processing and granule maturation are linked to pancreatic beta-cell failure during type 2 diabetes (T2D). Phosphatidylinositol transfer protein alpha (PITPNA) stimulates activity of phosphatidylinositol (PtdIns) 4-OH kinase to produce sufficient PtdIns-4-phosphate (PtdIns-4-P) in the trans-Golgi network to promote insulin granule maturation. PITPNA in beta-cells of T2D human subjects is markedly reduced suggesting its depletion accompanies beta-cell dysfunction. Conditional deletion of Pitpna in the beta-cells of Ins-Cre;Pitpnaflox/flox mice leads to hyperglycemia resulting from decreased glucose-stimulated insulin secretion (GSIS) and reduced pancreatic beta-cell mass. Furthermore, PITPNA silencing in human islets confirmed its role in PtdIns-4-P synthesis and led to impaired insulin granule maturation and docking, GSIS, and proinsulin processing with evidence of ER stress. Restoration of PITPNA in islets of T2D human subjects reversed these beta-cell defects and identify PITPNA as a critical target linked to beta-cell failure in T2D.

cell biology↗

bioRxiv2021

Biomechanical interactions of Schistosoma mansoni eggs with vascular endothelial cells facilitate egg extravasation

The eggs of the parasitic blood fluke, Schistosoma, are the main drivers of the chronic pathologies associated with schistosomiasis, a disease of poverty afflicting approximately 220 million people worldwide. Eggs laid by Schistosoma mansoni in the bloodstream of the host are encapsulated by vascular endothelial cells (VECs), the first step in the migration of the egg from the blood stream into the lumen of the gut and eventual exit from the body. The biomechanics associated with encapsulation and extravasation of the egg are poorly understood. We demonstrate that S. mansoni eggs induce VECs to form two types of membrane extensions during encapsulation; filopodia that probe eggshell surfaces and intercellular nanotubes that presumably facilitate VEC communication. Encapsulation efficiency, the number of filopodia and intercellular nanotubes, and the length of these structures depend on the eggs vitality and, to a lesser degree, its maturation state. During encapsulation, live eggs induce VEC contractility and membranous structures formation, in a Rho/ROCK pathway-dependent manner. Using elastic hydrogels embedded with fluorescent microbeads as substrates to culture VECs, live eggs induce VECs to exert significantly greater contractile forces during encapsulation than dead eggs, which leads to 3D deformations on both the VEC monolayer and the flexible substrate underneath. These significant mechanical deformations cause the VEC monolayer tension to fluctuate with eventual rupture of VEC junctions, thus facilitating egg transit out of the blood vessel. Overall, our data on the mechanical interplay between host VECs and the schistosome egg improve our understanding of how this parasite manipulates its immediate environment to maintain disease transmission.

microbiology↗

bioRxiv2021

Cyclic mechanical stresses alter erythrocyte membrane composition and microstructure and trigger macrophage phagocytosis

Red blood cells (RBCs) are cleared from the circulation when they become damaged or display aging signals targeted by macrophages. This process occurs mainly in the spleen, where blood flows through submicrometric constrictions called inter-endothelial slits (IES), subjecting RBCs to large-amplitude deformations. In this work, we circulated RBCs through microfluidic devices containing microchannels that replicate the IES. The cyclic mechanical stresses experienced by the cells affected their biophysical properties and molecular composition, accelerating cell aging. Specifically, RBCs quickly transitioned to a more spherical, less deformable phenotype that hindered microchannel passage, causing hemolysis. This transition was associated with the release of membrane vesicles, which self-extinguished as the spacing between membrane-cytoskeleton linkers became tighter. Proteomics analysis of the mechanically aged RBCs revealed significant losses of essential proteins involved in antioxidant protection, gas transport, and cell metabolism. Finally, we show that these changes made mechanically aged RBCs more susceptible to macrophage phagocytosis. These results provide a comprehensive model to explain how physical stress induces RBC clearance in the spleen.

bioengineering↗

bioRxiv2021

Accurate Virus Identification with Interpretable Raman Signatures by Machine Learning

Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device coupled with label-free Raman Spectroscopy holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning approach applied to recognize the virus based on its Raman spectrum. In this paper, we present a machine learning analysis on Raman spectra of human and avian viruses. A Convolutional Neural Network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A vs. type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and non-enveloped viruses, and 99% for differentiating avian coronavirus (infectious bronchitis virus, IBV) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups (e.g. amide, amino acid, carboxylic acid) we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses. The accurate and interpretable machine learning model developed for Raman virus identification presents promising potential in a real-time virus detection system. Significance StatementA portable micro-fluidic platform for virus capture promises rapid enrichment and label-free optical identification of viruses by Raman spectroscopy. A large Raman dataset collected on a variety of viruses enables the training of machine learning (ML) models capable of highly accurate and sensitive virus identification. The trained ML models can then be integrated with the portable device to provide real-time virus detection and identification capability. We validate this conceptual framework by presenting highly accurate virus type and subtype identification results using a convolutional neural network to classify Raman spectra of viruses.

biophysics↗

bioRxiv2020

A balance between matrix deformation and the coordination of turning events governs directed neutrophil migration in 3-D matrices

Three-dimensional (3-D) neutrophil migration is essential for immune surveillance and inflammatory responses. During 3-D migration, especially through extravascular spaces, neutrophils rely on frontal protrusions and rear contractions to squeeze and maneuver through extracellular matrices containing narrow pores. However, the role of matrix density and the cells ability to probe and remodel matrix pores during 3-D chemotaxis are far from being understood. We investigated these processes by tracking the trajectories of over 20,000 neutrophils in a 3-D migration device containing collagen matrices of varying concentrations and analyzing the shape of these trajectories at multiple scales. Additionally, we quantified the transient 3-D matrix deformations caused by the migrating cells. The mean pore size of our reconstituted collagen matrices decreased when the collagen concentration ([col]) was increased. In low-[col] matrices, neutrophils exerted large transient deformations and migrated in relatively straight trajectories. In contrast, they were not able to appreciably deform high- [col] matrices and adapted to this inability by turning more often to circumvent these narrow matrix pores. While this adaptation resulted in slower migration, the cells were able to balance the more frequent turning with the long-range directional bias necessary for chemotaxis. Based on our statistical analysis of cell trajectories, we postulate that neutrophils achieve this balance by using matrix obstacles as pivoting points to steer their motion towards the chemoattractant. Inhibiting myosin-II contractility or Arp2/3-mediated pseudopod protrusions not only compromised the cells ability to deform the matrix, but also made them switch to increased turning in more restrictive matrices when compared to untreated control cells. Both myosin-II contractility and Arp2/3-mediated branched polymerization of actin played a role in fast migration, but Arp2/3 was also crucial for neutrophils when coordinating the orientations of successive turns to prevent veering away from the chemotactic path. These results may contribute to an improved understanding of the mechanisms employed by migrating neutrophils in confined 3-D environments, as well as the molecular and environmental regulators for maintaining persistent motion.

biophysics↗

bioRxiv2019

Three-dimensional Monolayer Stress Microscopy

Many biological processes involve the collective generation and transmission of mechanical stresses across cell monolayers. In these processes, the monolayer undergoes lateral deformation and bending due to the tangential and normal components of the cell-generated stresses. Monolayer Stress Microscopy (MSM) methods have been developed to measure the intracellular stress distribution in cell monolayers. However, current methods assume plane monolayer geometry and neglect the contribution of bending to the intracellular stresses.\n\nThis work introduces a three-dimensional (3D) MSM method that calculates monolayer stress from measurements of the 3D traction stresses exerted by the cells on a flexible substrate. The calculation is carried out by imposing equilibrium of forces and moments in the monolayer, subject to external loads given by the 3D traction stresses. The equilibrium equations are solved numerically, and the algorithm is validated for synthetic loads with known analytical solutions.\n\nWe present 3D-MSM measurements of monolayer stress in micropatterned islands of endothelial cells of different sizes and shapes. These data indicate that intracellular stresses caused by lateral deformation emerge collectively over long distances; they increase with the distance from the island edge until they reach a constant value that is independent of island size. On the other hand, bending-induced intracellular stresses are more concentrated spatially and remain confined to within 1-2 cell lengths of bending sites. The magnitude of these bending stresses is highest at the edges of the cell islands, where they can exceed the intracellular stresses caused by lateral deformations. Our data from non-patterned monolayers suggests that biomechanical perturbations far away from monolayer edges also cause significant localized alterations in bending tension. The localized effect of bending-induced stresses may be important in processes like cellular extravasation, which are accompanied by significant normal deflections of a cell monolayer (i.e. the endothelium), and which require localized changes in monolayer permeability.

biophysics↗

bioRxiv2019

Quantifying the mechanics of locomotion of the schistosome pathogen with respect to changes in its physical environment

Schistosomiasis is a chronic and morbid disease of poverty affecting approximately 200 million people worldwide. Mature schistosome flatworms wander in the hosts hepatic portal and mesenteric venous system where they encounter a range of blood flow conditions and geometrical confinement. However, the mechanisms that support schistosome locomotion and underlie the pathogens adaptation to its physical environment are largely unknown. By combining microfabrication and traction force microscopy, we developed various in vitro assays to quantify the mechanics of locomotion of adult male S. mansoni in different physiologically relevant conditions. We show that in unconfined settings, the parasite undergoes two-anchor marching mediated by the coordinated action of its oral and ventral suckers. This mode of locomotion is maintained when the worm faces an external flow, to which it responds by adjusting the strength of its suckers. In geometrically confined conditions, S. mansoni switches to a different crawling modality by generating retrograde peristaltic waves along its body, a mechanism shared with terrestrial and marine worms. But while the surface of most worms has backward-pointing bristles that rectify peristaltic waves and facilitate forward locomotion, S mansoni has isotropically oriented tubercles. This requires tight coordination between muscle contraction and substrate friction but confers S. mansoni the ability to reverse its direction of locomotion without turning its body, which is likely advantageous to maneuver in narrow bore vessels. We show that the parasite can also coordinate the action of its suckers with its peristaltic body contractions to increase crawling speed. Throughout this study, we report on a number of biomechanical parameters to quantify the motility of adult schistosomes (e.g. sucker grabbing strength, rate of detachment under flow, peristaltic wave properties and traction stresses). The new series of in vitro assays make it possible to quantify key phenotypical aspects of S. mansoni motility that could guide the discovery of new drugs to treat schistosomiasis.

biophysics↗

bioRxiv2017

Cell surface vimentin is involved in matrix stiffness-dependent infection of endothelial cells by Listeria monocytogenes

Extracellular matrix (ECM) stiffness is one of many mechanical forces acting on mammalian adherent cells that influence cellular function. We have addressed the open question of how ECM stiffness might alter the susceptibility of host cells to infection by bacterial pathogens. We manufactured hydrogels of varying physiologically-relevant stiffness and seeded human microvascular endothelial cells (HMEC-1) on them. We then infected HMEC-1 with the bacterial pathogen Listeria monocytogenes (Lm) and found that adhesion of Lm onto host cells increases monotonically with increasing matrix stiffness, an effect that requires the activity of focal adhesion kinase (FAK). We identified cell surface vimentin as a candidate surface receptor mediating stiffness-dependent adhesion of Lm to HMEC-1, and demonstrated that bacterial infection of these host cells is decreased when surface vimentin is perturbed. Our results provide the first evidence that ECM stiffness can mediate the susceptibility of host cells to bacterial infection.

microbiology↗