Theoretical analysis of the magnetocardiographic pattern for reentry wave propagation in a three-dimensional human heart model

We present a computational study of reentry wave propagation using electrophysiological models of human cardiac cells and the associated magnetic field map of a human heart. We examined the details of magnetic field variation and related physiological parameters for reentry waves in two-dimensional (2-D) human atrial tissue and a three-dimensional (3-D) human ventricle model. A 3-D mesh system representing the human ventricle was reconstructed from the surface geometry of a human heart. We used existing human cardiac cell models to simulate action potential (AP) propagation in atrial tissue and 3-D ventricular geometry, and a finite element method and the Galerkin approximation to discretize the 3-D domain spatially. The reentry wave was generated using an S1-S2 protocol. The calculations of the magnetic field pattern assumed a horizontally layered conductor for reentry wave propagation in the 3-D ventricle. We also compared the AP and magnetocardiograph (MCG) magnitudes during reentry wave propagation to those during normal wave propagation. The temporal changes in the reentry wave motion and magnetic field map patterns were also analyzed using two well-known MCG parameters: the current dipole direction and strength. The current vector in a reentry wave forms a rotating spiral. We delineated the magnetic field using the changes in the vector angle during a reentry wave, demonstrating that the MCG pattern can be helpful for theoretical analysis of reentry waves.     

On the freezing and identification of lipid monolayer 2-D arrays for cryoelectron microscopy

Lipid monolayers provide a convenient vehicle for the crystallization of biological macromolecules for 3-D electron microscopy. Although numerous examples of 3-D images from 2-D protein arrays have been described from negatively stained specimens, only six structures have been done from frozen-hydrated specimens. We describe here a method that makes high quality frozen-hydrated specimens of lipid monolayer arrays for cryoelectron microscopy. The method uses holey carbon films with patterned holes for monolayer recovery, blotting and plunge freezing to produce thin aqueous films which cover >90% of the available grid area. With this method, even specimens with relatively infrequent crystals can be screened using automated data collection techniques. Though developed for microscopic examination of 2-D arrays, the method may have wider application to the preparation of single particle specimens for 3-D image reconstruction.     

Optimal design of bio-hybrid systems with a hollow fiber scaffold: model analysis of oxygen diffusion/consumption

The oxygen distribution in various bio-hybrid systems composed of cellular tissue on an artificial scaffold was estimated by mathematically modeling the oxygen consumption and diffusion. Mathematical models were established for practical systems such as bio-hybrid artificial liver (BAL) and bio-hybrid blood vessels, and the calculated results were compared with corresponding experimental data. Analysis of a spherical organoid (“spheroid”) composed of hepatic cells suggested that the oxygen consumption rate in hepatocyte spheroids incubated in a BAL is one or two orders of magnitude larger than the total average value that had been calculated for various organs. A model was established for a BAL system on a scaffold of commercially available hollow fiber (typical inner and outer radii of 150 and 200 μm) to determine the optimal conditions under which the hepatocytes can be packed as closely as possible into the hollow fiber lumen while still maintaining viability without falling into oxygen deficiency. A model of bio-hybrid blood vessels formed by vascular endothelial cells incubated on the inner wall of a hollow fiber scaffold was used to estimate the maximum thickness of viable endothelial tissue under various conditions of outer partial oxygen pressure and different sizes and permeabilities of the hollow fiber scaffold. The model suggested that the oxygen supply becomes quite restricted when the hollow fiber membrane is thicker than 100 μm; the thickness of the endothelium in a 500 μm-thick hollow fiber membrane was estimated to be 7 μm at most, even when the membrane permeability was as large as that of the culture medium.     

Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays

We report here the development and characterization of protein microarrays fabricated on nanoengineered 3-D polyelectrolyte thin films (PET) deposited on glass slide by consecutive adsorption of polyelectrolytes via self-assembly technique. Antibodies or antigens were immobilized in the PET-coated glass slides by electrostatic adsorption and entrapment of porous structure of the 3-D polymer film and thus establishing a platform for parallel analysis. Both antigen and antibody microarrays were fabricated on the PET-coated slides, and direct and indirect immunoassays on protein microarrays for multiple-analyte detection were demonstrated. Microarrays produced on these PET-coated slides have consistent spot morphology and provide performance features needed for proteomic analysis. The protein microarrays on the PET films provide LOD as low as 6 pg/mL and dynamic ranges up to three orders of magnitude, which are wider than the protein microarrays fabricated on aldehyde and poly-L-lysine functionalized slides. The PET films constructed by self-assembly technique in aqueous solution is green chemistry based, cost-effective method to generate 3-D thin film coatings on glass surface, and the coated slide is well suited for immobilizing many types of biological molecules so that a wide variety of microarray formats can be developed on this type of slide.     

Immobilization of Bacillus licheniformis α-amylase onto reactive polymer films

Alpha-amylase was covalently immobilized onto maleic anhydride copolymer films preserving activity. The initial activity of the immobilized layers strongly depended on the immobilization solution, and on the physicochemical properties of the copolymer film. Higher enzyme loading (quantified by amino acid analysis using HPLC) and activity (measured by following starch hydrolysis) were attainable onto hydrophilic, highly swelling 3-D poly(ethylene-alt-maleic anhydride) (PEMA) copolymer films, while immobilization onto hydrophobic poly(octadecene-alt-maleic anhydride) (POMA) copolymer films resulted in low content enzyme layers and lower activity. No significant activity was lost upon dehydration/re-hydration or storage of enzyme containing PEMA copolymer layers in deionised water for up to 48 h. In contrast, α-amylase decorated POMA films suffered a significant activity loss under those conditions. The distinct behaviours may be attributed to the different intrinsic physicochemical properties of the copolymer films. The compact, hydrophobic POMA films possibly favours hydrophobic interactions between the hydrophobic moieties of the protein and the surface, which may result in conformational changes, and consequent loss of activity. Surprisingly, residual activity was found after harsh treatments of active α-amylase PEMA based layers revealing that immobilization onto the hydrophilic polymer films improved the stability of the enzyme.     

Modeling of spherical fluorescent glucose microsensor systems: design of enzymatic smart tattoos

A two-substrate mathematical model of microspherical optical enzymatic glucose sensors is presented. The sensors are based on the well-known oxidation of glucose by glucose oxidase, and are constructed by the encapsulation of glucose oxidase within hydrogel microspheres coated with ultrathin polyelectrolyte multilayer films. In order to measure glucose via changes in oxygen concentration, a fluorescent oxygen indicator is co-encapsulated with the enzyme. The model was used to predict the temporal and spatial distributions of glucose and oxygen within the sphere for step increases in bulk glucose concentration. In addition, the model was used to observe the effect of varying sensor parameters, namely sphere size, film thickness, enzyme concentration, and mass transport of substrate and co-substrate within the sphere and film coatings, on the response of the sensors. A major finding was that the application of {PSS/PAH} films as thin as 12 nm can drastically improve the sensor performance over uncoated sensors based on calcium alginate microspheres. The model is proposed as an important tool for a priori design of these complex sensor structures.     

A model of calcium activation of the cardiac thin filament

The cardiac thin filament regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin and tropomyosin. Over the past several decades, many details of the structure and function of the cardiac thin filament and its components have been elucidated. We propose a dynamic, complete model of the thin filament that encompasses known structures of cardiac troponin, tropomyosin, and actin and show that it is able to capture key experimental findings. By performing molecular dynamics simulations under two conditions, one with calcium bound and the other without calcium bound to site II of cardiac troponin C (cTnC), we found that subtle changes in structure and protein contacts within cardiac troponin resulted in sweeping changes throughout the complex that alter tropomyosin (Tm) dynamics and cardiac troponin--actin interactions. Significant calcium-dependent changes in dynamics occur throughout the cardiac troponin complex, resulting from the combination of the following: structural changes in the N-lobe of cTnC at and adjacent to sites I and II and the link between them; secondary structural changes of the cardiac troponin I (cTnI) switch peptide, of the mobile domain, and in the vicinity of residue 25 of the N-terminus; secondary structural changes in the cardiac troponin T (cTnT) linker and Tm-binding regions; and small changes in cTnC-cTnI and cTnT-Tm contacts. As a result of these changes, we observe large changes in the dynamics of the following regions: the N-lobe of cTnC, the mobile domain of cTnI, the I-T arm, the cTnT linker, and overlapping Tm. Our model demonstrates a comprehensive mechanism for calcium activation of the cardiac thin filament consistent with previous, independent experimental findings. This model provides a valuable tool for research into the normal physiology of cardiac myofilaments and a template for studying cardiac thin filament mutations that cause human cardiomyopathies.     

Recognition of conformational changes in beta-lactoglobulin by molecularly imprinted thin films

Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein beta-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic acid on quartz crystal microbalance chips. Enhanced rebinding of the template isoform was observed in all cases when compared to the binding of nontemplate isoforms over the concentration range of 1-100 microg mL(-1). Furthermore, it was observed that the greater the changes in the secondary structure of the template protein the lower the binding of native BLG challenges to the imprint, suggesting a strong steric influence in the recognition system. This feasibility study is a first demonstration of molecular imprints for recognition of distinct conformations of the same protein.     

A 2-D model of flow-induced alterations in the geometry, structure, and properties of carotid arteries

Evidence from diverse investigations suggests that arterial growth and remodeling correlates well with changes in mechanical stresses from their homeostatic values. Ultimately, therefore, there is a need for a comprehensive theory that accounts for changes in the 3-D distribution of stress within the arterial wall, including residual stress, and its relation to the mechanisms of mechanotransduction. Here, however, we consider a simpler theory that allows competing hypotheses to be tested easily, that can provide guidance in the development of a 3-D theory, and that may be useful in modeling solid-fluid interactions and interpreting clinical data. Specifically, we present a 2-D constrained mixture model for the adaptation of a cylindrical artery in response to a sustained alteration in flow. Using a rule-of-mixtures model for the stress response and first order kinetics for the production and removal of the three primary load-bearing constituents within the wall, we illustrate capabilities of the model by comparing responses given complete versus negligible turnover of elastin. Findings suggest that biological constraints may result in suboptimal adaptations, consistent with reported observations. To build upon this finding, however, there is a need for significantly more data to guide the hypothesis testing as well as the formulation of specific constitutive relations within the model.     

Graphical analysis of mass and anisotropy changes observed by plasmon-waveguide resonance spectroscopy can provide useful insights into membrane protein function

Plasmon-waveguide resonance spectroscopy is a recently developed optical method that allows characterization of mass and structural changes in two-dimensionally ordered thin films (e.g., proteolipid membranes) deposited onto a sensor surface. Full analysis of these systems involves fitting theoretical curves (obtained using Maxwell's equations) to experimental spectra measured using s- and p-polarized excitation. This allows values to be obtained for refractive indices and optical extinction coefficients in these two directions, as well as a value for film thickness, thereby providing information about mass density and anisotropy changes. This is a time-consuming process that works well for simple systems in which only a single conformational event occurs, but cannot distinguish between events involving multiple conformations that proceed either sequentially or in a parallel series of events. This article describes a graphical method that can distinguish between mass density and anisotropy changes in a simpler, more rapid procedure, even for processes that proceed via multiple conformational events. This involves measurement of plasmon-waveguide resonance spectral shifts obtained upon molecular interactions occurring in deposited films with both s- and p-polarized excitation, and transforming these from an (s-p) coordinate system into a (mass-structure) coordinate system. This procedure is illustrated by data obtained upon the binding of a small peptide, penetratin, to solid-supported lipid bilayer membranes.     

Biophysical models of the heart electrical activity

Based on the fundamental knowledge of the space-temporal organization of extracellular electrical fields of the myocardium, a system for 3-D computer modeling of the cardiac electrical activity at different structural levels of the object is being developed at the Institute of Theoretical and Experimental Biophysics. The system is based on the earlier proposed and modified biophysical model of the electrocardiosignal genesis represented by a double electrical layer along the surface of the electrically active myocardium. The system combines the model for activation and repolarization of the heart ventricles; the advanced model for the evaluation of parameters of the cardiac electric field, which makes it possible to derive model electrocardiosignals both in the direct regime of calculation of the potentials and in the regime of calculation of electrocardiosignals from preliminarily determined components of the multipole equivalent electrical heart generator; a database for the model parameters and their combinations in the form of cards of simulated "patients", and a database of modeled electrocardiosignals. In the present paper (first from three within the framework of the problem), simulation methods in electrocardiology are briefly described and a biophysical model of the heart electrical activity is presented, which has made up the basis of the system for computer modeling of forward and inverse problems of the cardiac electric field. The parameters of the model are electrophysiological, anatomical, and biophysical characteristics of the heart.     

Spectral analysis of chromatin and its components in the vacuum ultraviolet region of the spectrum

Electronic absorption spectra of thin films of chromatin and chromatin components in ultraviolet (140-280 nm) were investigated. The absorption coefficients mu (lambda) of chromatin, nucleosomes with and without histone H1, total histones (TH), DNA were compared. The spectra of nucleosomes and chromatin differ from summary spectra of DNA + TH. The lack of additivity of absorption coefficients at different wavelengths may be explained by different conformational changes of free DNA, TH and DNA, TH in nucleosomes and chromatin during the process of drying aqueous solutions for the preparations of thin films. The obtained mu (lambda) values are necessary for the estimation of the DNA and TH parts of absorption in chromatin and nucleosomes in the investigations of UV and VUV irradiation damages.     

An orthotropic viscoelastic model for the passive myocardium: continuum basis and numerical treatment

This study deals with the viscoelastic constitutive modeling and the respective computational analysis of the human passive myocardium. We start by recapitulating the locally orthotropic inner structure of the human myocardial tissue and model the mechanical response through invariants and structure tensors associated with three orthonormal basis vectors. In accordance with recent experimental findings the ventricular myocardial tissue is assumed to be incompressible, thick-walled, orthotropic and viscoelastic. In particular, one spring element coupled with Maxwell elements in parallel endows the model with viscoelastic features such that four dashpots describe the viscous response due to matrix, fiber, sheet and fiber-sheet fragments. In order to alleviate the numerical obstacles, the strictly incompressible model is altered by decomposing the free-energy function into volumetric-isochoric elastic and isochoric-viscoelastic parts along with the multiplicative split of the deformation gradient which enables the three-field mixed finite element method. The crucial aspect of the viscoelastic formulation is linked to the rate equations of the viscous overstresses resulting from a 3-D analogy of a generalized 1-D Maxwell model. We provide algorithmic updates for second Piola–Kirchhoff stress and elasticity tensors. In the sequel, we address some numerical aspects of the constitutive model by applying it to elastic, cyclic and relaxation test data obtained from biaxial extension and triaxial shear tests whereby we assess the fitting capacity of the model. With the tissue parameters identified, we conduct (elastic and viscoelastic) finite element simulations for an ellipsoidal geometry retrieved from a human specimen.     

根瘤感受样基因的进化: 结构歧异与功能分化

豆科植物百脉根(Lotus japonicus)的根瘤感受基因Nin与根瘤的早期发育有关。Nin的同源基因(Nin-like基因)功能上涉及氮代谢过程。从完成测序的豆科和非豆科植物基因组中获取Nin-like基因并进行系统发育分析。在此基础上, 追踪基因和蛋白质结构的歧异式样, 尝试建立结构歧异和功能分化的联系。通过比较, 新的Nin-like基因被鉴别。系统发育分析不仅重现了以前分辨的直系同源群(分支I、II和III), 且识别了它们之间的姐妹群关系。Nin-like基因的结构呈现多样性, 支持系统发育分析的结果。水稻OsNLP5基因缺乏内含子, 可能起源于基因返座事件。NIN-like蛋白结构域组织和功能位点在不同分支中存在差异, 提示它们的功能发生了分化。根瘤固氮植物NIN-like蛋白的GAF结构域中存在一个显著变异区, 三级建模分析显示这个变异区对应于百脉根非固氮NIN-like蛋白的一段保守构象, 这一变异可能使豆科植物具有根瘤固氮能力。研究结果为阐明Nin-like基因的功能提供了新的研究思路。     

A Probabilistic Model of RNA Conformational Space

The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling procedure. Both are only partly solved problems. Here, we focus on the problem of conformational sampling. The current state of the art solution is based on fragment assembly methods, which construct plausible conformations by stringing together short fragments obtained from experimental structures. However, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.     

Circular dichroism and Fourier transform infrared spectroscopic studies on self-assembly of tetrapeptide derivative in solution and solvated film.

Aggregation of the hydrophobic peptide derivative Boc-Ala-Ile-Ile-Gly-OMe (1) was examined in methanol solution and in solvated film states. Formation of the peptide by self-assembly was evidenced using fluorescence [Mg salt of 8-anilino-naphthalenesulfonic acid (ANS) as an external probe] and circular dichroism (CD) spectroscopic techniques. In solution, peptide 1 formed as a stable aggregate at a concentration around 3 x 10(-4)m. The peptide gelled into a thin film for which we carried out CD and Fourier transform infrared (FTIR) measurements. Our spectroscopic study on peptide films at differing methanol concentrations indicates that the helical content of the peptide decreases with decreasing methanol concentration in solvated films. However, by reducing the methanol concentration we were able to observe a conformational transition from a predominantly helical turn to a beta-sheet structure via a random coil conformation. Our study focused on the aggregation of the alpha-helical turn-forming peptide derivative, which shows conformational transition on changing solvent concentration in the film form.     

Estimation of variance in single-particle reconstruction using the bootstrap technique

Density maps of a molecule obtained by single-particle reconstruction from thousands of molecule projections exhibit strong changes in local definition and reproducibility, as a consequence of conformational variability of the molecule and non-stoichiometry of ligand binding. These changes complicate the interpretation of density maps in terms of molecular structure. A three-dimensional (3-D) variance map provides an effective tool to assess the structural definition in each volume element. In this work, the different contributions to the 3-D variance in a single-particle reconstruction are discussed, and an effective method for the estimation of the 3-D variance map is proposed, using a bootstrap technique of sampling. Computations with test data confirm the viability, computational efficiency, and accuracy of the method under conditions encountered in practical circumstances.     

Development of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) fibers for skin tissue engineering: effects of topography, mechanical, and chemical stimuli

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), a biodegradable polyester, was electrospun to form defect-free fibers with high surface-area-to-volume ratio for skin regeneration. Several parameters such as solvent ratio, polymer concentration, applied voltage, flow rate, and tip-to-target distance were optimized to achieve defect-free morphology. The average diameter of the PHBV fibers was 724 ± 91 nm. PHBV was also solvent-cast to form 2-D films, and its mechanical properties, porosity, and degradation rates were compared with PHBV fibers. Our results demonstrate that PHBV fibers exhibited higher porosity, increased ductility, and faster degradation rate when compared with PHBV 2-D films (p < 0.05). In vitro studies with PHBV fibers and 2-D films were carried out to evaluate the adhesion, viability, proliferation, and gene expression of human skin fibroblasts. Cells adhered and proliferated on both PHBV fibers and 2-D films. However, the proliferation of cells on the surface of PHBV fibers was comparable to tissue culture polystyrene (TCPS, control) (p > 0.05). The gene expression of collagen I and elastin was significantly up-regulated when compared with TCPS control, whereas collagen III was down-regulated on PHBV fibers and 2-D film after 14 days in culture. The less ductile PHBV 2-D films showed higher levels of elastin expression. Furthermore, the PHBV fibers in the presence and absence of an angiogenesis factor (R-Spondin 1) were evaluated for their wound healing capacity in a rat model. The wound contracture in R-Spondin-1-loaded PHBV fibers was found to be significantly higher when compared with PHBV fibers alone after 7 days (p < 0.05). Furthermore, the presence of fibers promoted an increase in collagen and aided re-epithelialization. Thus our results demonstrate that the topography and mechanical and chemical stimuli have a pronounced influence on the cell proliferation, gene expression, and wound healing.     

Bioluminescence resonance energy transfer reveals ligand-induced conformational changes in CXCR4 homo- and heterodimers

Homo- and heterodimerization have emerged as prominent features of G-protein-coupled receptors with possible impact on the regulation of their activity. Using a sensitive bioluminescence resonance energy transfer system, we investigated the formation of CXCR4 and CCR2 chemokine receptor dimers. We found that both receptors exist as constitutive homo- and heterodimers and that ligands induce conformational changes within the pre-formed dimers without promoting receptor dimer formation or disassembly. Ligands with different intrinsic efficacies yielded distinct bioluminescence resonance energy transfer modulations, indicating the stabilization of distinct receptor conformations. We also found that peptides derived from the transmembrane domains of CXCR4 inhibited activation of this receptor by blocking the ligand-induced conformational transitions of the dimer. Taken together, our data support a model in which chemokine receptor homo- and heterodimers form spontaneously and respond to ligand binding as units that undergo conformational changes involving both protomers even when only one of the two ligand binding sites is occupied.     

Vitamin D: structure-function analyses and the design of analogs.

There is continuing and emerging new interest in the development of vitamin D analogs resulting from the recognition that analogs of 1 alpha,25-dihydroxyvitamin D3 [1 alpha,25-(OH)2D3] may be therapeutically useful. Side chain analogs of this steroid hormone are of particular interest because a family of lead structures have recently emerged for possible use in the treatment of certain types of cancers and skin diseases. Because of the chaotic array of side chain structures which exhibit useful therapeutic indices for these purposes, a more systematic approach towards developing intelligible structure-function information needs development. Accordingly, a method has been devised to analyze analogs as to their side chain topology based on identifying specific occupancy volumes through conformational analysis. Dot maps have been constructed as an indication of the volume in space which the side chain of 1 alpha,25-(OH)2-D3 or analogs is permitted to occupy. Volume exclusion analyses based on comparison of structural and biological data for 1 alpha,25-(OH)2-D3 and analogs are anticipated to lead to a more cogent model for drug design. A cautionary note on the limitations of this approach is discussed.