Biology subjects

Johnson, R. T.

Publications and source records attributed to Johnson, R. T..

9 recordsLinked to original sources

bioRxiv2026

Estimating Muscle Parameters via Hierarchical Bayesian Inference

Musculoskeletal models are widely used to relate muscle mechanics to movement patterns in biomechanics. Accurate estimation of muscle parameters is essential for building individualized models, yet most rely on generic parameters derived from cadaveric data that do not reflect subject-specific properties critical to force generation. Here, we introduce a hierarchical Bayesian framework that leverages surface electromyography (EMG) and torque data from isometric elbow tasks to estimate subject-specific muscle parameters, overcoming limitations of generic parameter sets. This approach accounts for both inter-individual variability and uncertainty in measurement and model structure. The model infers six key parameters per subject, including flexor and extensor muscle strength, tendon slack length, moment arm geometry, and nonlinear EMG-to-activation relationships. We estimated model parameters for 14 young, healthy adults performing isometric elbow flexion and extension at multiple joint angles and torque levels. The six-parameter hierarchical-Bayesian musculoskeletal model accurately reproduced measured net elbow torque (R{superscript 2} = 0.96) and outperformed simpler configurations. Muscle strength parameters varied substantially across individuals, from approximately 1.0 to 3.5. On average, participants exhibited about twice those of the OpenSim 26 generic model. In contrast, tendon slack length estimates varied minimally across subjects. Bilateral testing revealed moderate correlations between left- and right-arm parameters, supporting the models ability to capture subject-specific anatomical features. Cross-validation confirmed robust predictive performance, and convergence diagnostics indicated reliable sampling. Compared to traditional EMG-driven or imaging-based personalization methods, our approach quantifies uncertainty, enables partial pooling across subjects, and avoids reliance on invasive or time-intensive measurements. The framework is extensible to dynamic tasks and adaptable to clinical populations, including individuals post-stroke. These results demonstrate that hierarchical Bayesian inference can robustly personalize musculoskeletal models and advance our understanding of biomechanics.

bioengineering↗

bioRxiv2026

Lipoxins Regulate Intercalated Disk-Associated Signaling and Immune Remodeling in Dilated Cardiomyopathy

We investigated whether pro-resolving lipid mediators of the lipoxin family can attenuate fibrosis and inflammation in muscle LIM protein knockout (MLPko) mice, a model of dilated cardiomyopathy (DCM). Male and female MLPko mice received either vehicle or a mix of lipoxin-A4 and lipoxin-B4 three times per week for six weeks. Cardiac function was assessed using echocardiography, and fibrosis and DCM-associated cardiac signaling was evaluated through histology, immunofluorescence and immunoblot analyses. Flow cytometry and RNA sequencing (RNAseq) was performed to identify changes in cardiac gene expression and characterize macrophage subpopulations, respectively. Flow cytometry showed increased inflammatory CD11c+ M1-like macrophages and reduction of CD206+ M2-like macrophages in MLPko hearts compared to wild-type controls. Lipoxin treatment partially reversed the macrophage imbalance and showed mild improvements in cardiac physiology in MLPko males. RNAseq analyses revealed sex-dependent alterations in the expression of pro-fibrotic and inflammation-related genes, suggesting changes in extracellular matrix (ECM) integrity and composition, and to the adaptive immune response. Intriguingly, several ECM proteins showed unexpected localizations at cardiac intercalated disks, which are known to be involved in DCM etiology. Further analysis identified lipoxin-dependent reduction in the DCM-associated expression of intercalated disk components only in lipoxin-treated MLPko males. Lipoxins also modulated key cardiac signaling pathways in a sex-specific manner, including Erk1/2 and PKC-linked Ankrd1/Carp1, which is associated with DCM development in MLPko mice. While lipoxins do not directly reverse cardiac dysfunction or fibrosis in MLPko mice, they may provide sex-specific protective effects by modulating DCM-related cardiac signaling pathways and by influencing immune-cell populations.

cell biology↗

bioRxiv2022

A hydrogel-based model of aortic stiffness reveals that microtubules are novel regulators of smooth muscle cell hypertrophy

During ageing, the extracellular matrix of the aortic wall becomes more rigid. In response, VSMCs generate enhanced contractile forces. Our previous findings demonstrate that VSMC volume is enhanced in response to increased matrix rigidity, but our understanding of mechanisms regulating this process remain incomplete. In this current study, we show that microtubule stability in VSMCs is reduced in response to enhanced matrix rigidity via piezo1-mediated Ca2+ influx. Moreover, VSMC volume and Ca2+ flux was regulated by microtubule dynamics; microtubule stabilising agents reduced both VSMC volume and Ca2+ flux on rigid hydrogels, whereas microtubule destabilising agents increased VSMC volume and Ca2+ flux on pliable hydrogels. Finally, we show that disruption of the microtubule deacetylase HDAC6 uncoupled these processes and increased K40 alpha tubulin acetylation, VSMC volume and Ca2+ flux on pliable hydrogels, but did not alter VSMC microtubule stability. These findings uncover a microtubule stability switch that controls VSMC volume by regulating Ca2+ flux. Together, these data demonstrate that manipulation of microtubule stability can modify VSMC matrix rigidity response.

cell biology↗

bioRxiv2022

Endothelial neuropilin-1 and neuropilin-2 are essential for tumour angiogenesis

Neuropilin (NRP) expression is highly correlated with poor outcome in multiple cancer subtypes. As known co-receptors for vascular endothelial growth factor receptors (VEGFRs), core drivers of angiogenesis, past investigations have alluded to their functional roles in facilitating tumorigenesis by promoting invasive vessel growth. Despite this, it remains unclear as to whether NRP1 and NRP2 act in a synergistic manner to enhance pathological angiogenesis. Here we demonstrate, using NRP1ECKO, NRP2ECKO and NRP1/NRP2ECKO mouse models, that maximum inhibition of primary tumour development and angiogenesis is only achieved when both endothelial NRP1 and NRP2 are targeted simultaneously. Metastasis and secondary site angiogenesis were also significantly inhibited in NRP1/NRP2ECKO animals. Mechanistic studies revealed that co-depleting NRP1 and NRP2 in mouse-microvascular endothelial cells (ECs) stimulates rapid shuttling of VEGFR-2 to Rab7+ endosomes for proteosomal degradation. Our results highlight the importance of targeting both NRP1 and NRP2 to modulate tumour angiogenesis.

cancer biology↗

bioRxiv2021

Simulated hemiparesis increases optimal spatiotemporal gait asymmetry but not metabolic cost

Several neuromuscular impairments, such as weakness (hemiparesis), occur after an individual has a stroke, and these impairments primarily affect one side of the body more than the other. Predictive musculoskeletal modeling presents an opportunity to investigate how a specific impairment affects gait performance post-stroke. Therefore, our aim was to use to predictive simulation to quantify the spatiotemporal asymmetries and changes to metabolic cost that emerge when muscle strength is unilaterally reduced. We also determined how forced spatiotemporal symmetry affects metabolic cost. We modified a 2-D musculoskeletal model by uniformly reducing the peak isometric muscle force in all left-limb muscles. We then solved optimal control simulations of walking across a range of speeds by minimizing the sum of the cubed muscle excitations across all muscles. Lastly, we ran additional optimizations to test if reducing spatiotemporal asymmetry would result in an increase in metabolic cost. Our results showed that the magnitude and direction of effort-optimal spatiotemporal asymmetries depends on both the gait speed and level of weakness. Also, the optimal metabolic cost of transport was 1.25 m/s for the symmetrical and 20% weakness models but slower (1.00 m/s) for the 40% and 60% weakness models, suggesting that hemiparesis can account for a portion of the slower gait speed seen in people post-stroke. Adding spatiotemporal asymmetry to the cost function resulted in small increases (~4%) in metabolic cost. Overall, our results indicate that spatiotemporal asymmetry may be optimal for people post-stroke, who have asymmetrical neuromuscular impairments. Additionally, the effect of speed and level of weakness on spatiotemporal asymmetry may explain the well-known heterogenous distribution of spatiotemporal asymmetries observed in the clinic. Future work could extend our results by testing the effects of other impairments on optimal gait strategies, and therefore build a more comprehensive understanding of the gait patterns in people post-stroke. Author SummaryA stroke causes damage to the brain. This typically results in several changes to the nervous and muscular (neuromuscular) system that change how people post-stroke tend to walk and perform other tasks. Individuals post-stroke tend to walk with an asymmetrical motion and expend more energy while walking than other age-matched individuals. We still do not understand how each specific change to the neuromuscular system is linked with changes in walking patterns, in part because it is difficult to test one individual change at a time in people. Instead, we can use a mathematical model of the musculoskeletal system that represents the individual changes to the muscular system that occur in people post-stroke. In this study, we modeled how a common change in people post-stroke (muscle weakness) can impact walking patterns. We found that the level of weakness and the walking speed affect the asymmetrical walking patterns of our models, but do not change the total energy cost. Overall, our study is one step towards better understanding how neuromuscular changes in people post-stroke affects walking patterns. This knowledge could be applied to identify rehabilitation strategies that are most likely to improve walking in people post-stroke.

bioengineering↗

bioRxiv2021

Using polyacrylamide hydrogels to model physiological aortic stiffness reveals that microtubules are critical regulators of isolated smooth muscle cell morphology and contractility.

Vascular smooth muscle cells (VSMCs) are the predominant cell type in the medial layer of the aortic wall and normally exist in a quiescent, contractile phenotype where actomyosin-derived contractile forces maintain vascular tone. However, VSMCs are not terminally differentiated and can dedifferentiate into a proliferative, synthetic phenotype. Actomyosin force generation is essential for the function of both phenotypes. Whilst much is already known about the mechanisms of VSMC actomyosin force generation, existing assays are either low throughput and time consuming, or qualitative and inconsistent. In this study, we use polyacrylamide hydrogels, tuned to mimic the physiological stiffness of the aortic wall, in a VSMC contractility assay. Isolated VSMC area decreases following stimulation with the contractile agonists angiotensin II or carbachol. Importantly, the angiotensin II induced reduction in cell area correlated with increased traction stress generation. Inhibition of actomyosin activity using blebbistatin or Y-27632 prevented angiotensin II mediated changes in VSMC morphology, suggesting that changes in VSMC morphology and actomyosin activity are core components of the contractile response. Furthermore, we show that microtubule stability is an essential regulator of isolated VSMC contractility. Treatment with either colchicine or paclitaxel uncoupled the morphological and/or traction stress responses of angiotensin II stimulated VSMCs. Our findings support the tensegrity model and we demonstrate that microtubules act to balance the actomyosin-derived traction stress generation and regulate the morphological responses of VSMCs.

cell biology↗

bioRxiv2021

The Effects of Posture on the Three-Dimensional Gait Mechanics of Human Walking in Comparison to Bipedal Chimpanzees

Humans walk with an upright posture on extended limbs during stance and with a double-peaked vertical ground reaction force. Our closest living relatives, chimpanzees, are facultative bipeds that walk with a crouched posture on flexed, abducted hind limbs and with a single-peaked vertical ground reaction force. Differences in human and bipedal chimpanzee three-dimensional kinematics have been well quantified; however, it is unclear what the independent effects of using a crouched posture are on three-dimensional gait mechanics for humans, and how they compare with chimpanzees. Understanding the relationships between posture and gait mechanics, with known differences in morphology between species, can help researchers better interpret the effects of trait evolution on bipedal walking. We quantified pelvis and lower limb three-dimensional kinematics and ground reaction forces as humans adopted a series of upright and crouched postures and compared them with data from bipedal chimpanzee walking. Human crouched posture gait mechanics were more similar to bipedal chimpanzee gait than normal human walking, especially in sagittal plane hip and knee angles. However, there were persistent differences between species, as humans walked with less transverse plane pelvis rotation, less hip abduction, and greater peak horizontal ground reaction force in late stance than chimpanzees. Our results suggest that human crouched posture walking reproduces only a small subset of the characteristics of three-dimensional kinematics and ground reaction forces of chimpanzee walking, with the remaining differences likely due in large part to the distinct musculoskeletal morphologies of humans and chimpanzees. Summary StatementDifferences between human crouched posture gait and bipedal chimpanzee gait illustrate the limitations of using modern day humans to infer the evolution of hominin bipedalism.

bioengineering↗

bioRxiv2021

Using Bayesian Inference to Estimate Plausible Muscle Forces in Musculoskeletal Models

BackgroundMusculoskeletal modeling is currently a preferred method for estimating the muscle forces that underlie observed movements. However, these estimates are sensitive to a variety of assumptions and uncertainties, which creates difficulty when trying to interpret the muscle forces from musculoskeletal simulations. Here, we describe an approach that uses Bayesian inference to identify plausible ranges of muscle forces for a simple motion while representing uncertainty in the measurement of the motion and the objective function used to solve the muscle redundancy problem. MethodsWe generated a reference elbow flexion-extension motion by simulating a set of muscle excitation signals derived from the computed muscle control tool built into OpenSim. We then used a Markov Chain Monte Carlo (MCMC) algorithm to sample from a posterior probability distribution of muscle excitations that would result in the reference elbow motion trajectory. We constructed a prior over the excitation parameters which down-weighted regions of the parameter space with greater muscle excitations. We used muscle excitations to find the corresponding kinematics using OpenSim, where the error in position and velocity trajectories (likelihood function) was combined with the sum of the cubed muscle excitations integrated over time (prior function) to compute the posterior probability density. ResultsWe evaluated the muscle forces that resulted from the set of excitations that were visited in the MCMC chain (five parallel chains, 450,000 iterations per chain, runtime = 71 hours). The estimated muscle forces compared favorably with the reference motion from computed muscle control, while the elbow angle and velocity from MCMC matched closely with the reference with an average RMSE for angle and velocity equal to 0.008{degrees} and 0.18{degrees}/s, respectively. However, our rank plot analysis and potential scale reduction statistics, which we used to evaluate convergence of the algorithm, indicated that the parallel chains did not fully mix. ConclusionsWhile the results from this process are a promising step towards characterizing uncertainty in muscle force estimation, the computational time required to search the solution space with, and the lack of MCMC convergence indicates that further developments in MCMC algorithms are necessary for this process to become feasible for larger-scale models.

bioengineering↗

bioRxiv2017

The β3-integrin endothelial adhesome regulates microtubule dependent cell migration

Integrin {beta}3 is seen as a key anti-angiogenic target for cancer treatment due to its expression on neovasculature, but the role it plays in the process is complex; whether it is pro- or anti-angiogenic depends on the context in which it is expressed. To understand precisely {beta}3s role in regulating integrin adhesion complexes in endothelial cells, we characterised, by mass spectrometry, the {beta}3- dependent adhesome. We show that depletion of {beta}3-integrin in this cell type leads to changes in microtubule behaviour that control their migration. {beta}3- integrin regulates microtubule stability in endothelial cells through Rcc2/Anxa2 driven control of Rac1 activity. Our findings reveal that angiogenic processes, both in vitro and in vivo, are more sensitive to microtubule targeting agents when {beta}3-integrin levels are reduced.

cell biology↗