Systems biology and mechanics of growth

Automatic design of gene regulatory mechanisms for spatial pattern formation

Gene regulatory mechanisms (GRMs) control the formation of spatial and temporal expression patterns that can serve as regulatory signals for the development of complex shapes. Synthetic developmental biology aims to engineer such genetic circuits for understanding and producing desired multicellular spatial patterns. However, designing synthetic GRMs for complex, multi-dimensional spatial patterns is a current challenge due to the nonlinear interactions and feedback loops in genetic circuits. Here we present a methodology to automatically design GRMs that can produce any given two-dimensional spatial pattern. The proposed approach uses two orthogonal morphogen gradients acting as positional information signals in a multicellular tissue area or culture, which constitutes a continuous field of engineered cells implementing the same designed GRM. To efficiently design both the circuit network and the interaction mechanisms-including the number of genes necessary for the formation of the target spatial pattern-we developed an automated algorithm based on high-performance evolutionary computation. The tolerance of the algorithm can be configured to design GRMs that are either simple to produce approximate patterns or complex to produce precise patterns. We demonstrate the approach by automatically designing GRMs that can produce a diverse set of synthetic spatial expression patterns by interpreting just two orthogonal morphogen gradients. The proposed framework offers a versatile approach to systematically design and discover complex genetic circuits producing spatial patterns.

Lung Mechanics: A Review of Solid Mechanical Elasticity in Lung Parenchyma

The lung is the main organ of the respiratory system. Its purpose is to facilitate gas exchange (breathing). Mechanically, breathing may be described as the cyclic application of stresses acting upon the lung surface. These forces are offset by prominent stress-bearing components of lung tissue. These components result from the mechanical elastic properties of lung parenchyma. Various studies have been dedicated to understanding the macroscopic behaviour of parenchyma. This has been achieved through pressure-volume analysis, numerical methods, the development of constitutive equations or strain-energy functions, finite element methods, image processing and elastography. Constitutive equations can describe the elastic behaviour exhibited by lung parenchyma through the relationship between the macroscopic stress and strain. The research conducted within lung mechanics around the elastic and resistive properties of the lung has allowed scientists to develop new methods and equipment for evaluating and treating pulmonary pathogens. This paper establishes a review of mathematical studies conducted within lung mechanics, centering on the development and implementation of solid mechanics to the understanding of the mechanical properties of the lung. Under the classical theory of elasticity, the lung is said to behave as an isotropic elastic continuum undergoing small deformations. However, the lung has also been known to display heterogeneous anisotropic behaviour associated with large deformations. Therefore, focus is placed on the assumptions and development of the various models, their mechanical influence on lung physiology, and the development of constitutive equations through the classical and non-classical theory of elasticity. Lastly, we also look at lung blast mechanics. No explicit emphasis is placed on lung pathology.

Multi-Fidelity Gaussian Process Surrogate Modeling of Pediatric Tissue Expansion

Growth of skin in response to stretch is the basis for tissue expansion (TE), a procedure to gain new skin area for reconstruction of large defects. Unfortunately, complications and suboptimal outcomes persist because TE is planned and executed based on physician's experience and trial and error instead of predictive quantitative tools. Recently, we calibrated computational models of TE to a porcine animal model of tissue expansion, showing that skin growth is proportional to stretch with a characteristic time constant. Here, we use our calibrated model to predict skin growth in cases of pediatric reconstruction. Available from the clinical setting are the expander shapes and inflation protocols. We create low fidelity semi-analytical models and finite element models for each of the clinical cases. To account for uncertainty in the response expected from translating the models from the animal experiments to the pediatric population, we create multifidelity Gaussian process surrogates to propagate uncertainty in the mechanical properties and the biological response. Predictions with uncertainty for the clinical setting are essential to bridge our knowledge from the large animal experiments to guide and improve the treatment of pediatric patients. Future calibration of the model with patient-specific data-such as estimation of mechanical properties and area growth in the operating room-will change the standard for planning and execution of TE protocols.

PDE-constrained shape registration to characterize biological growth and morphogenesis from imaging data

We propose a PDE-constrained shape registration algorithm that captures the deformation and growth of biological tissue from imaging data. Shape registration is the process of evaluating optimum alignment between pairs of geometries through a spatial transformation function. We start from our previously reported work, which uses 3D tensor product B-spline basis functions to interpolate 3D space. Here, the movement of the B-spline control points, composed with an implicit function describing the shape of the tissue, yields the total deformation gradient field. The deformation gradient is then split into growth and elastic contributions. The growth tensor captures addition of mass, i.e. growth, and evolves according to a constitutive equation which is usually a function of the elastic deformation. Stress is generated in the material due to the elastic component of the deformation alone. The result of the registration is obtained by minimizing a total energy functional which includes: a distance measure reflecting similarity between the shapes, and the total elastic energy accounting for the growth of the tissue. We apply the proposed shape registration framework to study zebrafish embryo epiboly process and tissue expansion during skin reconstruction surgery. We anticipate that our PDE-constrained shape registration method will improve our understanding of biological and medical problems in which tissues undergo extreme deformations over time.

Patient-specific finite element analysis of heart failure and the impact of surgical intervention in pulmonary hypertension secondary to mitral valve disease

Pulmonary hypertension (PH), a chronic and complex medical condition affecting 1% of the global population, requires clinical evaluation of right ventricular maladaptation patterns under various conditions. A particular challenge for clinicians is a proper quantitative assessment of the right ventricle (RV) owing to its intimate coupling to the left ventricle (LV). We, thus, proposed a patient-specific computational approach to simulate PH caused by left heart disease and its main adverse functional and structural effects on the whole heart. Information obtained from both prospective and retrospective studies of two patients with severe PH, a 72-year-old female and a 61-year-old male, is used to present patient-specific versions of the Living Heart Human Model (LHHM) for the pre-operative and post-operative cardiac surgery. Our findings suggest that before mitral and tricuspid valve repair, the patients were at risk of right ventricular dilatation which may progress to right ventricular failure secondary to their mitral valve disease and left ventricular dysfunction. Our analysis provides detailed evidence that mitral valve replacement and subsequent chamber pressure unloading are associated with a significant decrease in failure risk post-operatively in the context of pulmonary hypertension. In particular, right-sided strain markers, such as tricuspid annular plane systolic excursion (TAPSE) and circumferential and longitudinal strains, indicate a transition from a range representative of disease to within typical values after surgery. Furthermore, the wall stresses across the RV and the interventricular septum showed a notable decrease during the systolic phase after surgery, lessening the drive for further RV maladaptation and significantly reducing the risk of RV failure.

Computational Systems Biology of Morphogenesis

Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis.

Bayesian calibration of a computational model of tissue expansion based on a porcine animal model

Tissue expansion is a technique used clinically to grow skin in situ to correct large defects. Despite its enormous potential, lack of fundamental knowledge of skin adaptation to mechanical cues, and lack of predictive computational models limit the broader adoption and efficacy of tissue expansion. In our previous work, we introduced a finite element model of tissue expansion that predicted key patterns of strain and growth which were then confirmed by our porcine animal model. Here we use the data from a new set of experiments to calibrate the computational model within a Bayesian framework. Four 10×10cm2 patches were tattooed in the dorsal skin of four 12 weeks-old minipigs and a total of six patches underwent successful tissue expander placement and inflation to 60cc for expansion times ranging from 1 h to 7 days. Six patches that did not have expanders implanted served as controls for the analysis. We find that growth can be explained based on the elastic deformation. The predicted area growth rate is k∈[0.02,0.08] [h-1]. Growth is anisotropic and reflects the anisotropic mechanical behavior of porcine dorsal skin. The rostral-caudal axis shows greater deformation than the transverse axis, and the time scale of growth in the rostral-caudal direction is given by rate parameters k1∈[0.04,0.1] [h-1] compared to k2∈[0.01,0.05] [h-1] in the transverse direction. Moreover, the calibration results underscore the high variability in biological systems, and the need to create probabilistic computational models to predict tissue adaptation in realistic settings. STATEMENT OF SIGNIFICANCE: Tissue expansion is a widely used technique in reconstructive surgery because it triggers growth of skin for the correction of large skin lesions and for breast reconstruction after mastectomy. Despite of its potential, complications and undesired outcomes persist due to our incomplete understanding of skin mechanobiology. Here we quantify the deformation and growth fields induced by an expander over 7 days in a porcine animal model and use these data to calibrate a computational model of skin growth using finite element simulations and a Bayesian framework. The calibrated model is a leap forward in our understanding skin growth, we now have quantitative understanding of this process: area growth is anisotropic and it is proportional to stretch with a characteristic rate constant of k∈[0.02,0.08] [h-1].

Stalling interkinetic nuclear migration in curved pseudostratified epithelium of developing cochlea

The bending of epithelial tubes is a fundamental process in organ morphogenesis, driven by various multicellular behaviours. The cochlea in the mammalian inner ear is a representative example of spiral tissue architecture where the continuous bending of the duct is a fundamental component of its morphogenetic process. Although the cochlear duct morphogenesis has been studied by genetic approaches extensively, it is still unclear how the cochlear duct morphology is physically formed. Here, we report that nuclear behaviour changes are associated with the curvature of the pseudostratified epithelium during murine cochlear development. Two-photon live-cell imaging reveals that the nuclei shuttle between the luminal and basal edges of the cell is in phase with cell-cycle progression, known as interkinetic nuclear migration, in the flat region of the pseudostratified epithelium. However, the nuclei become stationary on the luminal side following mitosis in the curved region. Mathematical modelling together with perturbation experiments shows that this nuclear stalling facilitates luminal-basal differential growth within the epithelium, suggesting that the nuclear stalling would contribute to the bending of the pseudostratified epithelium during the cochlear duct development. The findings suggest a possible scenario of differential growth which sculpts the tissue shape, driven by collective nuclear dynamics.

Developing a Lung Model in the Age of COVID-19: A Digital Image Correlation and Inverse Finite Element Analysis Framework

Pulmonary diseases, driven by pollution, industrial farming, vaping, and the infamous COVID-19 pandemic, lead morbidity and mortality rates worldwide. Computational biomechanical models can enhance predictive capabilities to understand fundamental lung physiology; however, such investigations are hindered by the lung’s complex and hierarchical structure, and the lack of mechanical experiments linking the load-bearing organ-level response to local behaviors. In this study we address these impedances by introducing a novel reduced-order surface model of the lung, combining the response of the intricate bronchial network, parenchymal tissue, and visceral pleura. The inverse finite element analysis (IFEA) framework is developed using 3-D digital image correlation (DIC) from experimentally measured non-contact strains and displacements from an ex-vivo porcine lung specimen for the first time. A custom-designed inflation device is employed to uniquely correlate the multiscale classical pressure-volume bulk breathing measures to local-level deformation topologies and principal expansion directions. Optimal material parameters are found by minimizing the error between experimental and simulation-based lung surface displacement values, using both classes of gradient-based and gradient-free optimization algorithms and by developing an adjoint formulation for efficiency. The heterogeneous and anisotropic characteristics of pulmonary breathing are represented using various hyperelastic continuum formulations to divulge compound material parameters and evaluate the best performing model. While accounting for tissue anisotropy with fibers assumed along medial-lateral direction did not benefit model calibration, allowing for regional material heterogeneity enabled accurate reconstruction of lung deformations when compared to the homogeneous model. The proof-of-concept framework established here can be readily applied to investigate the impact of assorted organ-level ventilation strategies on local pulmonary force and strain distributions, and to further explore how diseased states may alter the load-bearing material behavior of the lung. In the age of a respiratory pandemic, advancing our understanding of lung biomechanics is more pressing than ever before.

Mathematical Modelling of Residual-Stress Based Volumetric Growth in Soft Matter

Growth in nature is associated with the development of residual stresses and is in general heterogeneous and anisotropic at all scales. Residual stress in an unloaded configuration of a growing material provides direct evidence of the mechanical regulation of heterogeneity and anisotropy of growth. The present study explores a model of stress-mediated growth based on the unloaded configuration that considers either the residual stress or the deformation gradient relative to the unloaded configuration as a growth variable. This makes it possible to analyze stress-mediated growth without the need to invoke the existence of a fictitious stress-free grown configuration. Furthermore, applications based on the proposed theoretical framework relate directly to practical experimental scenarios involving the "opening-angle" in arteries as a measure of residual stress. An initial illustration of the theory is then provided by considering the growth of a spherically symmetric thick-walled shell subjected to the incompressibility constraint.

The Geometry of Incompatibility in Growing Soft Tissues: Theory and Numerical Characterization

Tissues in vivo are not stress-free. As we grow, our tissues adapt to different physiological and disease conditions through growth and remodeling. This adaptation occurs at the microscopic scale, where cells control the microstructure of their immediate extracellular environment to achieve homeostasis. The local and heterogeneous nature of this process is the source of residual stresses. At the macroscopic scale, growth and remodeling can be accurately captured with the finite volume growth framework within continuum mechanics, which is akin to plasticity. The multiplicative split of the deformation gradient into growth and elastic contributions brings about the notion of incompatibility as a plausible description for the origin of residual stress. Here we define the geometric features that characterize incompatibility in biological materials. We introduce the geometric incompatibility tensor for different growth types, showing that the constraints associated with growth lead to specific patterns of the incompatibility metrics. To numerically investigate the distribution of incompatibility measures, we implement the analysis within a finite element framework. Simple, illustrative examples are shown first to explain the main concepts. Then, numerical characterization of incompatibility and residual stress is performed on three biomedical applications: brain atrophy, skin expansion, and cortical folding. Our analysis provides new insights into the role of growth in the development of tissue defects and residual stresses. Thus, we anticipate that our work will further motivate additional research to characterize residual stresses in living tissue and their role in development, disease, and clinical intervention.

Novel Mechanical Strain Characterization of Ventilated ex vivo Porcine and Murine Lung using Digital Image Correlation

Respiratory illnesses, such as bronchitis, emphysema, asthma, and COVID-19, substantially remodel lung tissue, deteriorate function, and culminate in a compromised breathing ability. Yet, the structural mechanics of the lung is significantly understudied. Classical pressure-volume air or saline inflation studies of the lung have attempted to characterize the organ’s elasticity and compliance, measuring deviatory responses in diseased states; however, these investigations are exclusively limited to the bulk composite or global response of the entire lung and disregard local expansion and stretch phenomena within the lung lobes, overlooking potentially valuable physiological insights, as particularly related to mechanical ventilation. Here, we present a method to collect the first non-contact, full-field deformation measures of ex vivo porcine and murine lungs and interface with a pressure-volume ventilation system to investigate lung behavior in real time. We share preliminary observations of heterogeneous and anisotropic strain distributions of the parenchymal surface, associative pressure-volume-strain loading dependencies during continuous loading, and consider the influence of inflation rate and maximum volume. This study serves as a crucial basis for future works to comprehensively characterize the regional response of the lung across various species, link local strains to global lung mechanics, examine the effect of breathing frequencies and volumes, investigate deformation gradients and evolutionary behaviors during breathing, and contrast healthy and pathological states. Measurements collected in this framework ultimately aim to inform predictive computational models and enable the effective development of ventilators and early diagnostic strategies.

Introducing a Custom-Designed Volume-Pressure Machine for Novel Measurements of Whole Lung Organ Viscoelasticity and Direct Comparisons Between Positive- and Negative-Pressure Ventilation

Asthma, emphysema, COVID-19 and other lung-impacting diseases cause the remodeling of tissue structural properties and can lead to changes in conducting pulmonary volume, viscoelasticity, and air flow distribution. Whole organ experimental inflation tests are commonly used to understand the impact of these modifications on lung mechanics. Here we introduce a novel, automated, custom-designed device for measuring the volume and pressure response of lungs, surpassing the capabilities of traditional machines and built to range size-scales to accommodate both murine and porcine tests. The software-controlled system is capable of constructing standardized continuous volume-pressure curves, while accounting for air compressibility, yielding consistent and reproducible measures while eliminating the need for pulmonary degassing. This device uses volume-control to enable viscoelastic whole lung macromechanical insights from rate dependencies and pressure-time curves. Moreover, the conceptual design of this device facilitates studies relating the phenomenon of diaphragm breathing and artificial ventilation induced by pushing air inside the lungs. System capabilities are demonstrated and validated via a comparative study between ex vivo murine lungs and elastic balloons, using various testing protocols. Volume-pressure curve comparisons with previous pressure-controlled systems yield good agreement, confirming accuracy. This work expands the capabilities of current lung experiments, improving scientific investigations of healthy and diseased pulmonary biomechanics. Ultimately, the methodologies demonstrated in the manufacturing of this system enable future studies centered on investigating viscoelasticity as a potential biomarker and improvements to patient ventilators based on direct assessment and comparisons of positive- and negative-pressure mechanics.

Characterizing the viscoelasticity of extra- and intra-parenchymal lung bronchi

Pulmonary disease is known to cause remodeling of tissue structure, resulting in altered viscoelastic properties; yet the foundation for understanding this phenomenon is still nascent and will enable scientific insights regarding lung functionality. In order to characterize the viscoelastic response of pulmonary airways, uniaxial tensile experiments are conducted on porcine extra- and intra-parenchymal bronchial regions, measuring both axially and circumferentially oriented tissue. Anisotropic and heterogeneous effects on preconditioning and hysteresis are substantial, linking to energy dissipation expectancies. Stress relaxation is rheologically modeled using several classical configurations of discrete spring and dashpot elements; among them, Standard Linear Solid (SLS) and Maxwell-Weichart exhibit better fit performance. Enhanced fractional order derivative SLS (FSLS) model is also evaluated through use of a hybrid spring-pot of order α. FSLS outperforms the conventional models, demonstrating superior representation of the stress-relaxation curve's initial value and non-linear asymptotic decent. FSLS parameters exhibit notable orientation- and region-specific values, trending with observed tissue structural constituents, such as glycosaminoglycan and collagen. To the best of our knowledge, this work is the first to characterize proximal and distal bronchial energy efficiency and contextualize tissue biochemical composition in view of experimental measures and viscoelastic trends. Results provide a foundation for future investigations, particularly for understanding the role of viscoelasticity in diseased states.

Propagation of uncertainty in the mechanical and biological response of growing tissues using multi-fidelity Gaussian process regression

A key feature of living tissues is their capacity to remodel and grow in response to environmental cues. Within continuum mechanics, this process can be captured with the multiplicative split of the deformation gradient into growth and elastic contributions. The mechanical and biological response during tissue adaptation is characterized by inherent variability. Accounting for this uncertainty is critical to better understand tissue mechanobiology, and, moreover, it is of practical importance if we aim to develop predictive models for clinical use. However, the current gold standard in computational models of growth and remodeling remains the use of deterministic finite element (FE) simulations. Here we focus on tissue expansion, a popular technique in which skin is stretched by a balloon-like device inducing its growth. We construct FE models of tissue expansion with various levels of detail, and show that a sufficiently broad set of FE simulations from these models can be used to train an accurate and efficient multi-fidelity Gaussian process (GP) surrogate. The approach is not limited to simulation data, rather, it can fuse different kinds of data, including from experiments. The main appeal of the framework relies on the common experience that highly detailed models (or experiments) are more accurate but also more costly, while simpler models (or experiments) can be easily evaluated but are bound to have some error. In these situations, doing uncertainty analysis tasks with the high fidelity models alone is not feasible and, conversely, relying solely on low fidelity approximations is also undesirable. We show that a multi-fidelity GP outperforms the high fidelity GP and low fidelity GP when tested against the most detailed FE model. In turn, having trained the multi-fidelity GP model, we showcase the propagation of uncertainty from the mechanical and biological response parameters to the spatio-temporal growth outcomes. We expect that the methods and applications in this paper will enable future research in parameter calibration under uncertainty and uncertainty propagation in real clinical scenarios involving tissue growth and remodeling.

Mechanics of pulmonary airways: Linking structure to function through constitutive modeling, biochemistry, and histology

Breathing involves fluid-solid interactions in the lung; however, the lack of experimental data inhibits combining the mechanics of air flow to airway deformation, challenging the understanding of how biomaterial constituents contribute to tissue response. As such, lung mechanics research is increasingly focused on exploring the relationship between structure and function. To address these needs, we characterize mechanical properties of porcine airways using uniaxial tensile experiments, accounting for bronchial orientation- and location- dependency. Structurally-reinforced constitutive models are developed to incorporate the role of collagen and elastin fibers embedded within the extrafibrillar matrix. The strain-energy function combines a matrix description (evaluating six models: compressible NeoHookean, unconstrained Ogden, uncoupled Mooney-Rivlin, incompressible Ogden, incompressible Demiray and incompressible NeoHookean), superimposed with non-linear fibers (evaluating two models: exponential and polynomial). The best constitutive formulation representative of all bronchial regions is determined based on curve-fit results to experimental data, accounting for uniqueness and sensitivity. Glycosaminoglycan and collagen composition, alongside tissue architecture, indicate fiber form to be primarily responsible for observed airway anisotropy and heterogeneous mechanical behavior. To the authors' best knowledge, this study is the first to formulate a structurally-motivated constitutive model, augmented with biochemical analysis and microstructural observations, to investigate the mechanical function of proximal and distal bronchi. Our systematic pulmonary tissue characterization provides a necessary foundation for understanding pulmonary mechanics; furthermore, these results enable clinical translation through simulations of airway obstruction in disease, fluid-structure interaction insights during breathing, and potentially, predictive capabilities for medical interventions. STATEMENT OF SIGNIFICANCE: The advancement of pulmonary research relies on investigating the biomechanical response of the bronchial tree. Experiments demonstrating the non-linear, heterogeneous, and anisotropic material behavior of porcine airways are used to develop a structural constitutive model representative of proximal and distal bronchial behavior. Calibrated material parameters exhibit regional variation in biomaterial properties, initially hypothesized to originate from tissue constituents. Further exploration through biochemical and histological analysis indicates mechanical function is primarily governed by microstructural form. The results of this study can be directly used in finite element and fluid-structure interaction models to enable physiologically relevant and more accurate computational simulations aimed to help diagnose and monitor pulmonary disease.

Developmental origins and oncogenic pathways in malignant brain tumors

Brain tumors such as adult glioblastomas and pediatric high-grade gliomas or medulloblastomas are among the leading causes of cancer-related deaths, exhibiting poor prognoses with little improvement in outcomes in the past several decades. These tumors are heterogeneous and can be initiated from various neural cell types, contributing to therapy resistance. How such heterogeneity arises is linked to the tumor cell of origin and their genetic alterations. Brain tumorigenesis and progression recapitulate key features associated with normal neurogenesis; however, the underlying mechanisms are quite dysregulated as tumor cells grow and divide in an uncontrolled manner. Recent comprehensive genomic, transcriptomic, and epigenomic studies at single-cell resolution have shed new light onto diverse tumor-driving events, cellular heterogeneity, and cells of origin in different brain tumors. Primary and secondary glioblastomas develop through different genetic alterations and pathways, such as EGFR amplification and IDH1/2 or TP53 mutation, respectively. Mutations such as histone H3K27M impacting epigenetic modifications define a distinct group of pediatric high-grade gliomas such as diffuse intrinsic pontine glioma. The identification of distinct genetic, epigenomic profiles and cellular heterogeneity has led to new classifications of adult and pediatric brain tumor subtypes, affording insights into molecular and lineage-specific vulnerabilities for treatment stratification. This review discusses our current understanding of tumor cells of origin, heterogeneity, recurring genetic and epigenetic alterations, oncogenic drivers and signaling pathways for adult glioblastomas, pediatric high-grade gliomas, and medulloblastomas, the genetically heterogeneous groups of malignant brain tumors. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion Signaling Pathways > Cell Fate Signaling.

On the compressibility and poroelasticity of human and murine skin

A total of 37 human and 33 murine skin samples were subjected to uniaxial monotonic, cyclic, and relaxation experiments. Detailed analysis of the three-dimensional kinematic response showed that skin volume is significantly reduced as a consequence of a tensile elongation. This behavior is most pronounced in monotonic but persists in cyclic tests. The dehydration associated with volume loss depends on the osmolarity of the environment, so that tension relaxation changes as a consequence of modifying the ionic strength of the environmental bath. Similar to ex vivo observations, complementary in vivo stretching experiments on human volar forearms showed strong in-plane lateral contraction. A biphasic homogenized model is proposed which allows representing all relevant features of the observed mechanical response.

Mechanical properties of the airway tree: heterogeneous and anisotropic pseudoelastic and viscoelastic tissue responses

Airway obstruction and pulmonary mechanics remain understudied despite lung disease being the third cause of death in the United States. Lack of relevant data has led computational pulmonary models to infer mechanical properties from available material data for the trachea. Additionally, the time-dependent, viscoelastic behaviors of airways have been largely overlooked, despite their potential physiological relevance and utility as metrics of tissue remodeling and disease progression. Here, we address the clear need for airway-specific material characterization to inform biophysical studies of the bronchial tree. Specimens from three airway levels (trachea, large bronchi, and small bronchi) and two orientations (axial and circumferential) were prepared from five fresh pig lungs. Uniaxial tensile tests revealed substantial heterogeneity and anisotropy. Overall, the linear pseudoelastic modulus was significantly higher axially than circumferentially (30.5 ± 3.1 vs. 8.4 ± 1.1 kPa) and significantly higher among circumferential samples for small bronchi than for the trachea and large bronchi (12.5 ± 1.9 vs. 6.0 ± 0.6 and 6.6 ± 0.9 kPa). Circumferential samples exhibited greater percent stress relaxation over 300 s than their axial counterparts (38.0 ± 1.4 vs. 23.1 ± 1.5%). Axial and circumferential trachea samples displayed greater percent stress relaxation (26.4 ± 1.6 and 42.5 ± 1.7%) than corresponding large and small bronchi. This ex vivo pseudoelastic and viscoelastic characterization reveals novel anisotropic and heterogeneous behaviors and equips us to construct airway-specific constitutive relations. Our results establish necessary fundamentals for airway mechanics, laying the groundwork for future studies to extend to clinical questions surrounding lung injury, and further directly enables computational tools for lung disease obstruction predictions. NEW & NOTEWORTHY Understanding the mechanics of the lung is necessary for investigating disease progression. Trachea mechanics comprises the vast majority of ex vivo airway tissue characterization despite distal airways being the site of disease manifestation and occlusion. Furthermore, viscoelastic studies are scarce, whereas time-dependent behaviors could be potential physiological metrics of tissue remodeling. In this study, the critical need for airway-specific material properties is addressed, reporting bronchial tree anisotropic and heterogeneous material properties.

Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review

Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.

Elastosis during airway wall remodeling explains multiple co-existing instability patterns

Living structures can undergo morphological changes in response to growth and alterations in microstructural properties in response to remodeling. From a biological perspective, airway wall inflammation and airway elastosis are classical hallmarks of growth and remodeling during chronic lung disease. From a mechanical point of view, growth and remodeling trigger mechanical instabilities that result in inward folding and airway obstruction. While previous analytical and computational studies have focused on identifying the critical parameters at the onset of folding, few have considered the post-buckling behavior. All prior studies assume constant microstructural properties during the folding process; yet, clinical studies now reveal progressive airway elastosis, the degeneration of elastic fibers associated with a gradual stiffening of the inner layer. Here, we explore the influence of temporally evolving material properties on the post-bifurcation behavior of the airway wall. We show that a growing and stiffening inner layer triggers an additional subsequent bifurcation after the first instability occurs. Evolving material stiffnesses provoke failure modes with multiple co-existing wavelengths, associated with the superposition of larger folds evolving on top of the initial smaller folds. This phenomenon is exclusive to material stiffening and conceptually different from the phenomenon of period doubling observed in constant-stiffness growth. Our study suggests that the clinically observed multiple wavelengths in diseased airways are a result of gradual airway wall stiffening. While our evolving material properties are inspired by the clinical phenomenon of airway elastosis, the underlying concept is broadly applicable to other types of remodeling including aneurysm formation or brain folding.