Dependence of mechanical behavior of the murine tail disc on regional material properties: a parametric finite element study

In vivo rodent tail models are becoming more widely used for exploring the role of mechanical loading on the initiation and progression of intervertebral disc degeneration. Historically, finite element models (FEMs) have been useful for predicting disc mechanics in humans. However, differences in geometry and tissue properties may limit the predictive utility of these models for rodent discs. Clearly, models that are specific for rodent tail discs and accurately simulate the disc's transient mechanical behavior would serve as important tools for clarifying disc mechanics in these animal models. An FEM was developed based on the structure, geometry, and scale of the mouse tail disc. Importantly, two sources of time-dependent mechanical behavior were incorporated: viscoelasticity of the matrix, and fluid permeation. In addition, a novel strain-dependent swelling pressure was implemented through the introduction of a dilatational stress in nuclear elements. The model was then validated against data from quasi-static tension-compression and compressive creep experiments performed previously using mouse tail discs. Finally, sensitivity analyses were performed in which material parameters of each disc subregion were individually varied. During disc compression, matrix consolidation was observed to occur preferentially at the periphery of the nucleus pulposus. Sensitivity analyses revealed that disc mechanics was greatly influenced by changes in nucleus pulposus material properties, but rather insensitive to variations in any of the endplate properties. Moreover, three key features of the model-nuclear swelling pressure, lamellar collagen viscoelasticity, and interstitial fluid permeation-were found to be critical for accurate simulation of disc mechanics. In particular, collagen viscoelasticity dominated the transient behavior of the disc during the initial 2200 s of creep loading, while fluid permeation governed disc deformation thereafter. The FEM developed in this study exhibited excellent agreement with transient creep behavior of intact mouse tail motion segments. Notably, the model was able to produce spatial variations in nucleus pulposus matrix consolidation that are consistent with previous observations in nuclear cell morphology made in mouse discs using confocal microscopy. Results of this study emphasize the need for including nucleus swelling pressure, collagen viscoelasticity, and fluid permeation when simulating transient changes in matrix and fluid stress/strain. Sensitivity analyses suggest that further characterization of nucleus pulposus material properties should be pursued, due to its significance in steady-state and transient disc mechanical response.     

Comparative study of perturbations of peripheral markers in different stressors in rats

Stress has been implicated in the etiopathogenesis of several diseases. In the present study, the effects of acute (AS), chronic (CS), and chronic unpredictable stress (CUS) were studied on the ulcer index, adrenal gland mass, and biochemical and hormonal changes in rats. The stress was provided in the form of immobilization-immobilization for 150 min, once only, and for 10 consecutive days in CS and CUS. In CUS, animals received variable unpredictable stressors. Immediately after stress, animals were decapitated, blood was collected, and plasma was separated for the estimation of plasma glucose, triglyceride, cholesterol, creatine kinase (CK), corticosterone, and insulin. The adrenal gland and stomach were also dissected for mass and ulcer scoring, respectively. AS significantly increased the ulcer index, plasma glucose, CK, corticosterone, and insulin. CS and CUS significantly increased the ulcer index, adrenal gland mass, and corticosterone. In CS, a significant decrease in plasma triglyceride and cholesterol levels was found, but in CUS only cholesterol was decreased significantly. High CK activity and hyperglycemia maintain the energy demands of metabolism, and elevated corticosterone desensitizes the insulin receptor in AS. In CS and CUS, prolonged elevation of corticosterone shifts metabolism to utilization of lipids as a secondary substrate by gluconeogenesis. From our experiment, it is clear that AS causes maximum activation of energy metabolism, which becomes specific after habituation in prolonged CS. These biochemical manipulations in the body by using different types of stressors are good markers that can be of great use to understand, target, and manage stress-induced etiologies.     

Fluorinated graphene nanomaterial causes potential mechanical perturbations to a biomembrane

Journal of Molecular Modeling - Investigation of complexes of nanostructured materials and biomolecules has attracted much attention by various researchers as it can contribute to coherent growth...     

Amplitude effects of medio-lateral mechanical and visual perturbations on gait

Falls during walking are a major contributor to accidental deaths and injuries that can result in debilitating hospitalization costs, lost productivity, and diminished quality of life. To reduce these losses, we must develop a more profound understanding of the characteristic responses to perturbations similar to those encountered in daily life. This study addresses this issue by building on our earlier studies that examined mechanical and visual perturbations in the same environment by applying the same continuous pseudo-random perturbations at multiple (3 mechanical, 5 visual) amplitudes. Walking variability during mechanical perturbations increased significantly with amplitude for all subjects and differences as measured by variabilities of step width, COM position, and COM velocity. These parameters were the only ones sensitive to the presence of visual perturbations, but none of them changed significantly with perturbation amplitude. Additionally, visual perturbation effects were far less consistent across participants, with several who were essentially unaffected by visual perturbations at any level. The homogeneity of the mechanical perturbation effects demonstrates that human responses to mechanical perturbations are similar because they are driven by kinetics that require similar corrections that must be made in order to maintain balance. Conversely, responses to visual perturbations are driven by the perceived need to make corrections and this perception is not accurate enough to produce amplitude-related corrections, even for a single participant, nor is this perception consistent across individuals. This latter finding is likely to be relevant to future visual perturbation studies and the diagnosis and rehabilitation of gait and balance disorders.     

Dependence of the mechanical properties of a pullulan film on the preparation temperature

The mechanical properties of pullulan films prepared at various temperatures were investigated. The films prepared at high temperatures (40 degrees C and 60 degrees C; H-films) did not show any clear plastic deformation in tensile test, indicating that they were brittle. In contrast, those prepared at low temperatures (4 degrees C, 13 degrees C, and 25 degrees C; L-films) showed such deformation. The latter films had higher values for both tensile strength and elastic modulus than the former, indicating that the L-films were stiffer and more flexible than the H-films. Stretching the L-films clearly showed a shear deformation band inclined at 45 degrees to the stretching direction, indicating that they were amorphous.     

Canonical sensitivities: a useful tool to deal with large perturbations in metabolic network modeling

The dynamic range of metabolic models can be extended to deal with large perturbations by introducing the related concepts of "generalized" kinetic order and "canonical" sensitivities. Generalized kinetic orders are built as a well-defined non linear combination of the canonical sensitivities coefficients, which in turn are obtained by a least-squares regression on central composite factorial design data. In a such way, the whole domain of the operating variables is mapped without need to determine locally neither the first nor the second order model derivatives. The method was validated through numerical simulations, its predictions being compared with those coming from a Michaelis-Menten formalism taken as reference. In parallel, two variants of the Power-law formalism (S-system, least-squares GMA) also were tested. The canonical sensitivities method produced the widest range to predict metabolite concentrations and metabolic fluxes at the steady states. In addition, the variation pattern for the logarithmic gains and for the characteristic eigenvalues have been accurately determined from a unique overall model, being both required to make realistic analysis in metabolic engineering. The achieved information also can be expressed in terms of those typical coefficients derived from the Metabolic Control Analysis (MCA). Even if current first order Power-law or MCA formalisms were used, the canonical sensitivities approach provides a significant advantage, since complete sets of homologous, accurate, locally valid metabolic coefficients can be simultaneously recovered from the array proposed, being representative of the whole range of the operating variables instead of a unique nominal condition as is usual.     

Walking is not like reaching: evidence from periodic mechanical perturbations

The control architecture underlying human reaching has been established, at least in broad outline. However, despite extensive research, the control architecture underlying human locomotion remains unclear. Some studies show evidence of high-level control focused on lower-limb trajectories; others suggest that nonlinear oscillators such as lower-level rhythmic central pattern generators (CPGs) play a significant role. To resolve this ambiguity, we reasoned that if a nonlinear oscillator contributes to locomotor control, human walking should exhibit dynamic entrainment to periodic mechanical perturbation; entrainment is a distinctive behavior of nonlinear oscillators. Here we present the first behavioral evidence that nonlinear neuro-mechanical oscillators contribute to the production of human walking, albeit weakly. As unimpaired human subjects walked at constant speed, we applied periodic torque pulses to the ankle at periods different from their preferred cadence. The gait period of 18 out of 19 subjects entrained to this mechanical perturbation, converging to match that of the perturbation. Significantly, entrainment occurred only if the perturbation period was close to subjects' preferred walking cadence: it exhibited a narrow basin of entrainment. Further, regardless of the phase within the walking cycle at which perturbation was initiated, subjects' gait synchronized or phase-locked with the mechanical perturbation at a phase of gait where it assisted propulsion. These results were affected neither by auditory feedback nor by a distractor task. However, the convergence to phase-locking was slow. These characteristics indicate that nonlinear neuro-mechanical oscillators make at most a modest contribution to human walking. Our results suggest that human locomotor control is not organized as in reaching to meet a predominantly kinematic specification, but is hierarchically organized with a semi-autonomous peripheral oscillator operating under episodic supervisory control.     

The mechanical properties of trabecular bone: Dependence on anatomic location and function

In 1961, Evans and King documented the mechanical properties of trabecular bone from multiple locations in the proximal human femur. Since this time, many investigators have cataloged the distribution of trabecular bone material properties from multiple locations within the human skeleton to include femur, tibia, humerus, radius, vertebral bodies, and iliac crest. The results of these studies have revealed tremendous variations in material properties and anisotropy. These variations have been attributed to functional remodeling as dictated by Wolff's Law. Both linear and power functions have been found to explain the relationship between trabecular bone density and material properties. Recent studies have re-emphasized the need to accurately quantify trabecular bone architecture proposing several algorithms capable of determining the anisotropy, connectivity and morphology of the bone. These past studies, as well as continuing work, have significantly increased the accuracy of analytical and experimental models investigating bone, and bone/implant interfaces as well as enhanced our perspective towards understanding the factors which may influence bone formation or resorption.     

Insights into the structural perturbations of spliced variants of CD44: a modeling and simulation approach

Transient interactions between cancer stem cells and components of the tumor microenvironment initiate various signaling pathways crucial for carcinogenesis. Predominant hyaluronan (HA) receptor, CD44 is structurally and functionally one of the most variable cell surface receptors having the potential to generate a diverse repertory of CD44 isoforms by alternative splicing of variant exons and post-translational modifications. A structurally distinctive variant of CD44, CD44v10, has an inevitable role in malignant progression, invasion, and metastasis. This can be attributed to the binding of HA with CD44v10, which demonstrates a completely different behavioral pattern as compared to the other spliced variants of CD44 molecule. Absence of a comprehensively predicted crystal structure of human CD44s and CD44v10 is an impediment in understanding the resultant structural alterations caused by the binding of HA. Thus, in this study, we aim to predict the CD44s and CD44v10 structures to their closest native confirmation and study the HA binding-induced structural perturbations using homology modeling, molecular docking, and MD simulation approach. The results depicted that modeled 3D structures of CD44s and CD44v10 isoforms were found to be stable throughout MD simulations; however, a substantial decrease was observed in the binding affinity of HA with CD44v10 (?5.355 kcal/mol) as compared to CD44s. Furthermore, loss and gain of several H-bonds and hydrophobic interactions in CD44v10–HA complex during the simulation process not only elucidated the reason for decreased binding affinity for HA but also prompted toward the plausible role of HA-induced structural perturbations in occurrence and progression of carcinogenesis.     

Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study

The perturbations induced in a lipid bilayer by the presence of a transmembrane nanotube are investigated using coarse grained molecular dynamics. Meniscus formation by the lipids and tilting of the nanotube occur in response to hydrophobic mismatch, although these two effects do not compensate completely for the total mismatch. The lipid head-to-tail vector field is examined and shows strong ordering in the membrane plane regardless of the nanotube length. Molecular layering at the lipid-nanotube interface is reported. This study extends previous theoretical approaches to a more realistic setting.     

Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method

The mechanical properties of biomolecules play pivotal roles in regulating cellular functions. For instance, extracellular mechanical stimuli are converted to intracellular biochemical activities by membrane receptors and their downstream adaptor proteins during mechanotransduction. In general, proteins favor the conformation with the lowest free energy. External forces modify the energy landscape of proteins and drive them to unfolded or deformed conformations that are of functional relevance. Therefore, the study of the physical properties of proteins under external forces is of fundamental importance to understand their functions in cellular mechanics. Here, a coarse-grained computational model was developed to simulate the unfolding or deformation of proteins under mechanical perturbation. By applying this method to unfolding of previously studied proteins or protein fragments with external forces, we demonstrated that our results are quantitatively comparable to previous experimental or all-atom computational studies. The model was further extended to the problem of elastic deformation of large protein complexes formed between membrane receptors and their ligands. Our studies of binding between T cell receptor (TCR) and major histocompatibility complex (MHC) illustrated that stretching of MHC ligand initially lowers its binding energy with TCR, supporting the recent experimental report that TCR/MHC complex is formed through the catch-bond mechanism. Finally, the method was, for the first time, applied to pulling of an eight-cadherin cluster that was formed by their trans and cis binding interfaces. Our simulation results show that mechanical properties of adherens junctions are functionally important to cell adhesion.     

Interdisciplinary modeling: a case study of evolutionary economics

Biologists and economists use models to study complex systems. This similarity between these disciplines has led to an interesting development: the borrowing of various components of model-based theorizing between the two domains. A major recent example of this strategy is economists’ utilization of the resources of evolutionary biology in order to construct models of economic systems. This general strategy has come to be called “evolutionary economics” and has been a source of much debate among economists. Although philosophers have developed literatures on the nature of models and modeling, the unique issues surrounding this kind of interdisciplinary model building have yet to be independently investigated. In this paper, we utilize evolutionary economics as a case study in the investigation of more general issues concerning interdisciplinary modeling. We begin by critiquing the distinctions currently used within the evolutionary economics literature and propose an alternative carving of the conceptual terrain. We then argue that the three types of evolutionary economics we distinguish capture distinctions that will be important whenever resources of model-based theorizing are borrowed across distinct scientific domains. Our analysis of these model-building strategies identifies several of the unique methodological and philosophical issues that confront interdisciplinary modeling.     

Nonlinear mechanical modeling of cell adhesion

Cell adhesion, which is mediated by the receptor-ligand bonds, plays an essential role in various biological processes. Previous studies often described the force-extension relationship of receptor-ligand bond with linear assumption. However, the force-extension relationship of the bond is intrinsically nonlinear, which should have significant influence on the mechanical behavior of cell adhesion. In this work, a nonlinear mechanical model for cell adhesion is developed, and the adhesive strength was studied at various bond distributions. We find that the nonlinear mechanical behavior of the receptor-ligand bonds is crucial to the adhesive strength and stability. This nonlinear behavior allows more bonds to achieve large bond force simultaneously, and therefore the adhesive strength becomes less sensitive to the change of bond density at the outmost periphery of the adhesive area. In this way, the strength and stability of cell adhesion are soundly enhanced. The nonlinear model describes the cell detachment behavior better than the linear model.     

Impact of quarantine on the 2003 SARS outbreak: a retrospective modeling study

During the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak, traditional intervention measures such as quarantine and border control were found to be useful in containing the outbreak. We used laboratory verified SARS case data and the detailed quarantine data in Taiwan, where over 150,000 people were quarantined during the 2003 outbreak, to formulate a mathematical model which incorporates Level A quarantine (of potentially exposed contacts of suspected SARS patients) and Level B quarantine (of travelers arriving at borders from SARS affected areas) implemented in Taiwan during the outbreak. We obtain the average case fatality ratio and the daily quarantine rate for the Taiwan outbreak. Model simulations is utilized to show that Level A quarantine prevented approximately 461 additional SARS cases and 62 additional deaths, while the effect of Level B quarantine was comparatively minor, yielding only around 5% reduction of cases and deaths. The combined impact of the two levels of quarantine had reduced the case number and deaths by almost a half. The results demonstrate how modeling can be useful in qualitative evaluation of the impact of traditional intervention measures for newly emerging infectious diseases outbreak when there is inadequate information on the characteristics and clinical features of the new disease-measures which could become particularly important with the looming threat of global flu pandemic possibly caused by a novel mutating flu strain, including that of avian variety.     

Dependence of invadopodia function on collagen fiber spacing and cross-linking: computational modeling and experimental evidence

Invadopodia are subcellular organelles thought to be critical for extracellular matrix (ECM) degradation and the movement of cells through tissues. Here we examine invadopodia generation, turnover, and function in relation to two structural aspects of the ECM substrates they degrade: cross-linking and fiber density. We set up a cellular automaton computational model that simulates ECM penetration and degradation by invadopodia. Experiments with denatured collagen (gelatin) were used to calibrate the model and demonstrate the inhibitory effect of ECM cross-linking on invadopodia degradation and penetration. Incorporation of dynamic invadopodia behavior into the model amplified the effect of cross-linking on ECM degradation, and was used to model feedback from the ECM. When the model was parameterized with spatial fibrillar dimensions that closely matched the organization, in real life, of native ECM collagen into triple-helical monomers, microfibrils, and macrofibrils, little or no inhibition of invadopodia penetration was observed in simulations of sparse collagen gels, no matter how high the degree of cross-linking. Experimental validation, using live-cell imaging of invadopodia in cells plated on cross-linked gelatin, was consistent with simulations in which ECM cross-linking led to higher rates of both invadopodia retraction and formation. Analyses of invadopodia function from cells plated on cross-linked gelatin and collagen gels under standard concentrations were consistent with simulation results in which sparse collagen gels provided a weak barrier to invadopodia. These results suggest that the organization of collagen, as it may occur in stroma or in vitro collagen gels, forms gaps large enough so as to have little impact on invadopodia penetration/degradation. By contrast, dense ECM, such as gelatin or possibly basement membranes, is an effective obstacle to invadopodia penetration and degradation, particularly when cross-linked. These results provide a novel framework for further studies on ECM structure and modifications that affect invadopodia and tissue invasion by cells.     

Interaction of cardiotoxins with membranes: a molecular modeling study

Incorporation of beta-sheet proteins into membrane is studied theoretically for the first time, and the results are validated by the direct experimental data. Using Monte Carlo simulations with implicit membrane, we explore spatial structure, energetics, polarity, and mode of insertion of two cardiotoxins with different membrane-destabilizing activity. Both proteins, classified as P- and S-type cardiotoxins, are found to retain the overall "three-finger" fold interacting with membrane core and lipid/water interface by the tips of the "fingers" (loops). The insertion critically depends upon the structure, hydrophobicity, and electrostatics of certain regions. The simulations reveal apparently distinct binding modes for S- and P-type cardiotoxins via the first loop or through all three loops, respectively. This rationalizes an earlier empirical classification of cardiotoxins into S- and P-type, and provides a basis for the analysis of experimental data on their membrane affinities. Accomplished with our previous simulations of membrane alpha-helices, the computational method may be used to study partitioning of proteins with diverse folds into lipid bilayers.     

Short-term effect of silicone gel on peripheral nerves: a histologic study.

The effect of silicone gel on the peripheral nerve was studied in Sprague-Dawley rats. Silicone gel was placed either extraneurally (N = 36) adjacent to or injected directly in the sciatic nerve (N = 20). Nerve histology was studied every 2 weeks over a 20-week period. Extraneural silicone gel elicited an intense inflammatory response characterized initially by predominantly histiocytes with a few eosinophils, lymphocytes, and foreign-body giant cells. The cellular response peaked at 4 weeks, after which time collagen deposition increased and the thickness of the cellular infiltrate surrounding the gel decreased. The gel was temporarily contained by the inflammatory response, but throughout the time course of the study, gel migration and breakup into smaller droplets occurred. Each droplet appeared to initiate the inflammation-fibrosis cycle anew. Perineural fibrosis was marked by 20 weeks, but there was no penetration of the epineurium by the gel. Intraneurally injected silicone gel also caused a delayed, but similar inflammatory response, eventually followed by fibrosis surrounding the gel. Intraneural gel tended to remain in larger droplets and did not migrate over the duration of this study. No direct evidence of gel toxicity to peripheral nerves was observed in either the extraneural or intraneural gel groups despite the initial intense inflammatory response and subsequent fibrosis.     

Some clouds have a silver lining: paradoxes of anthropogenic perturbations from study cases on long-lived social birds

In recent centuries and above all over the last few decades, human activities have generated perturbations (from mild to very severe or catastrophes) that, when added to those of natural origin, constitute a global threat to biodiversity. Predicting the effects of anthropogenic perturbations on species and communities is a great scientific challenge given the complexity of ecosystems and the need for detailed population data from both before and after the perturbations. Here we present three cases of well-documented anthropogenic severe perturbations (different forms of habitat loss and deterioration influencing fertility and survival) that have affected three species of birds (a raptor, a scavenger and a waterbird) for which we possess long-term population time series. We tested whether the perturbations caused serious population decline or whether the study species were resilient, that is, its population dynamics were relatively unaffected. Two of the species did decline, although to a relatively small extent with no shift to a state of lower population numbers. Subsequently, these populations recovered rapidly and numbers reached similar levels to before the perturbations. Strikingly, in the third species a strong breakpoint took place towards greater population sizes, probably due to the colonization of new areas by recruits that were queuing at the destroyed habitat. Even though it is difficult to draw patterns of resilience from only three cases, the study species were all long-lived, social species with excellent dispersal and colonization abilities, capable of skipping reproduction and undergoing a phase of significant long-term population increase. The search for such patterns is crucial for optimizing the limited resources allocated to conservation and for predicting the future impact of planned anthropogenic activities on ecosystems.