Interstrand Spacing Research Articles

Experimental Characterization and Finite Element Modeling of the Effects of 3D Bioplotting Process Parameters on Structural and Tensile Properties of Polycaprolactone (PCL) Scaffolds

In this study we characterized the process–structure interactions in melt extrusion-based 3D bioplotting of polycaprolactone (PCL) and developed predictive models to enable the efficient design and processing of scaffolds for tissue engineering applications. First, the effects of pneumatic extrusion pressure (0.3, 0.4, 0.5, 0.6 N/mm2), nozzle speed (0.1, 0.4, 1.0, 1.4 mm/s), strand lay orientation (0°, 45°, 90°, 135°), and strand length (10, 20, 30 mm) on the strand width were investigated and a regression model was developed to map strand width to the two significant parameters (extrusion pressure and nozzle speed; p < 0.05). Then, proliferation of NIH/3T3 fibroblast cells in scaffolds with two different stand widths fabricated with different combinations of the two significant parameters was assessed over 7 days, which showed that the strand width had a significant effect on proliferation (p < 0.05). The effect of strand lay orientation (0° and 90°) on tensile properties of non-porous PCL specimens was determined and was found to be significantly higher for specimens with 0° lay orientation (p < 0.05). Finally, these data were used to develop and experimentally validate a finite element model for a porous PCL specimen with 1:1 ratio of inter-strand spacing to strand width.

3D bioprinting of anisotropic engineered tissue constructs with ultrasonically induced cell patterning

As 3D bioprinting continues to evolve as a promising alternative to engineer complex human tissues in-vitro, there is a need to augment bioprinting processes to achieve the requisite cellular and extracellular organizational characteristics found in the original tissues. While the cell distribution within bioinks is typically homogeneous, incorporating appropriate cellular patterning within the bioprinted constructs is an essential first step towards the eventual formation of anisotropically organized tissue matrix essential to its biomechanical form and function. This study describes a new bioprinting technique that uses ultrasonic standing bulk acoustic waves (SBAW) to organize cells into controllable anisotropic patterns within viscous bioinks while maintaining high cell viability. First, we develop a 3D computational model to discern the SBAW pressure pattern in response to multiple ultrasonic frequencies (0.71–2 MHz). We then experimentally analyze the patterns and viabilities of human adipose-derived stem cells (hASC) and human osteosarcoma cells (MG63) in alginate as a function of the SBAW frequency. Computational results indicate the formation of parallel pressure strands with higher pressure amplitudes near the bottom of the deposited layer, which is corroborated by experimental images of cell patterning. The inter-strand spacing is found to be affected by the frequency (p < 0.0001), while an interaction effect between the cell type and frequency governs the width of the strands (p = 0.02). Further, we demonstrate the synergistic bioprinting and SBAW-induced patterning of hASC within alginate and gelatin methacrylate (GelMA) constructs in tandem with chemical and photo-crosslinking, respectively. Pertinent cellular patterning and viability of at least 80 % were noted in the alginate and GelMA constructs across the experimental design space. Finally, we demonstrate the vat photo-polymerization-based bioprinting of a 3-layered GelMA construct with hASC strand lay pattern of 0-45-90° across the layers. This work represents a step forward in advancing bioprinting capabilities to achieve biomimetic tissue constructs.

Characterizing the Process Physics of Ultrasound-Assisted Bioprinting

3D bioprinting has been evolving as an important strategy for the fabrication of engineered tissues for clinical, diagnostic, and research applications. A major advantage of bioprinting is the ability to recapitulate the patient-specific tissue macro-architecture using cellular bioinks. The effectiveness of bioprinting can be significantly enhanced by incorporating the ability to preferentially organize cellular constituents within 3D constructs to mimic the intrinsic micro-architectural characteristics of native tissues. Accordingly, this work focuses on a new non-contact and label-free approach called ultrasound-assisted bioprinting (UAB) that utilizes acoustophoresis principle to align cells within bioprinted constructs. We describe the underlying process physics and develop and validate computational models to determine the effects of ultrasound process parameters (excitation mode, excitation time, frequency, voltage amplitude) on the relevant temperature, pressure distribution, and alignment time characteristics. Using knowledge from the computational models, we experimentally investigate the effect of selected process parameters (frequency, voltage amplitude) on the critical quality attributes (cellular strand width, inter-strand spacing, and viability) of MG63 cells in alginate as a model bioink system. Finally, we demonstrate the UAB of bilayered constructs with parallel (0°–0°) and orthogonal (0°–90°) cellular alignment across layers. Results of this work highlight the key interplay between the UAB process design and characteristics of aligned cellular constructs, and represent an important next step in our ability to create biomimetic engineered tissues.

Mechanical properties of tissue formed in vivo are affected by 3D-bioplotted scaffold microarchitecture and correlate with ECM collagen fiber alignment

ABSTRACTPurpose: Musculoskeletal soft tissues possess highly aligned extracellular collagenous networks that provide structure and strength. Such an organization dictates tissue-specific mechanical properties but can be difficult to replicate by engineered biological substitutes. Nanofibrous electrospun scaffolds have demonstrated the ability to control cell-secreted collagen alignment, but concerns exist regarding their scalability for larger and anatomically relevant applications. Additive manufacturing processes, such as melt extrusion-based 3D-Bioplotting, allow fabrication of structurally relevant scaffolds featuring highly controllable porous microarchitectures.Materials and Methods: In this study, we investigate the effects of 3D-bioplotted scaffold design on the compressive elastic modulus of neotissue formed in vivo in a subcutaneous rat model and its correlation with the alignment of ECM collagen fibers. Polycaprolactone scaffolds featuring either 100 or 400 µm interstrand spacing were implanted for 4 or 12 weeks, harvested, cryosectioned, and characterized using atomic-force-microscopy-based force mapping.Results: The compressive elastic modulus of the neotissue formed within the 100 µm design was significantly higher at 4 weeks (p < 0.05), but no differences were observed at 12 weeks. In general, the tissue stiffness was within the same order of magnitude and range of values measured in native musculoskeletal soft tissues including the porcine meniscus and anterior cruciate ligament. Finally, a significant positive correlation was noted between tissue stiffness and the degree of ECM collagen fiber alignment (p < 0.05) resulting from contact guidance provided by scaffold strands.Conclusion: These findings demonstrate the significant effects of 3D-bioplotted scaffold microarchitectures in the organization and sub-tissue-level mechanical properties of ECM in vivo.

Engineering 3D-Bioplotted scaffolds to induce aligned extracellular matrix deposition for musculoskeletal soft tissue replacement

ABSTRACTPurpose: Tissue engineering and regenerative medicine approaches have the potential to overcome the challenges associated with current treatment strategies for meniscus injuries. 3D-Bioplotted scaffolds are promising, but have not demonstrated the ability to guide the formation of aligned collagenous matrix in vivo, which is critical for generating functional meniscus tissue. In this study, we evaluate the ability of 3D-Bioplotted scaffold designs with varying interstrand spacing to induce the deposition of aligned matrix in vivo. Materials and Methods: 3D-Bioplotted polycaprolactone scaffolds with 100, 200, or 400 μm interstrand spacing were implanted subcutaneously in a rat model for 4, 8, or 12 weeks. Scaffolds were harvested, paraffin-embedded, sectioned, and stained to visualize cell nuclei and collagen. Quantitative image analysis was used to evaluate cell density, matrix fill, and collagen fiber alignment within the scaffolds. Results: By 4 weeks, cells had infiltrated the innermost scaffold regions. Similarly, collagenous matrix filled interstrand regions nearly completely by 4 weeks. By 12 weeks, aligned collagen was present in all scaffolds. Generally, alignment along the scaffold strands increased over time for all three interstrand spacing groups. Distribution of collagen fiber alignment angles narrowed as interstrand spacing decreased. Conclusions: 3D-Bioplotted scaffolds allow for complete cell infiltration and collagenous matrix production throughout the scaffold. The ability to use interstrand spacing as a means of controlling the formation of aligned collagen in vivo was demonstrated, which helps establish a design space for scaffold-based meniscus tissue engineering.

DNA bending-induced phase transition of encapsidated genome in phage

The DNA structure in phage capsids is determined by DNA–DNA interactions and bending energy. The effects of repulsive interactions on DNA interaxial distance were previously investigated, but not the effect of DNA bending on its structure in viral capsids. By varying packaged DNA length and through addition of spermine ions, we transform the interaction energy from net repulsive to net attractive. This allowed us to isolate the effect of bending on the resulting DNA structure. We used single particle cryo-electron microscopy reconstruction analysis to determine the interstrand spacing of double-stranded DNA encapsidated in phage λ capsids. The data reveal that stress and packing defects, both resulting from DNA bending in the capsid, are able to induce a long-range phase transition in the encapsidated DNA genome from a hexagonal to a cholesteric packing structure. This structural observation suggests significant changes in genome fluidity as a result of a phase transition affecting the rates of viral DNA ejection and packaging.

AC loss measurements in pancake coils wound with 2G tapes and Roebel cable: dependence on spacing between turns/strands

AC loss measurements in five single pancake coils wound with 4 mm wide commercial high temperature superconductor wires were carried out to investigate the dependence of coil AC loss on separation between the superconductor layers in the neighbouring coil turns (g) and coil turn number (N) for a given number of ampere-turns NI. The highest frequency was set at approximately 1 kHz. The AC losses measured at different frequencies agreed well with each other. AC loss in the coils with the same N increases with decreasing g. When g is increased to 1.5 times the tape width (6 mm), the loss level is similar to that in an isolated wire. Transport AC loss per unit length in the pancake coils increases with increasing turn number. However, when g is increased to 1.5 times the tape width, the loss level in the coils with different turn number is almost the same. This indicates that, at the same NI, a coil with greater N is advantageous, even considering the conductor length difference. Therefore to achieve a given level of NI for a coil and minimize AC loss, we should favour coils with more turns. Coil AC loss can be measured using voltage taps attached to copper blocks outside a coil with reasonable accuracy. This is important for measuring AC loss in a coil with a complicated structure where voltage taps are not able to be attached inside the coil. AC loss in a nine-turn pancake coil wound with a 5 m long 9/2 Roebel cable (i.e. with 9 mm × 2 mm width strands) was measured using voltage loops arranged in each Roebel strand in the central turn of the coil. The AC loss in the coil was compared with two straight 9/2 Roebel cables with and without spacing between the strands. The combination of inter-strand spacing and turn spacing is an effective way to reduce AC loss in a single pancake coil wound with a Roebel cable.

Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids

DNA toroids that form inside the bacteriophage capsid present different shapes according to whether they are formed by the addition of spermine or polyethylene glycol to the bathing solution. Spermine-DNA toroids present a convex, faceted section with no or minor distortions of the DNA interstrand spacing with respect to those observed in the bulk, whereas polyethylene glycol-induced toroids are flattened to the capsid inner surface and show a crescent-like, nonconvex shape. By modeling the energetics of the DNA toroid using a free-energy functional composed of energy contributions related to the elasticity of the wound DNA, exposed surface DNA energy, and adhesion between the DNA and the capsid, we established that the crescent shape of the toroidal DNA section comes from attractive interactions between DNA and the capsid. Such attractive interactions seem to be specific to the PEG condensation process and are not observed in the case of spermine-induced DNA condensation.

Discrete molecular dynamics simulations of peptide aggregation.

We study the aggregation of peptides using the discrete molecular dynamics simulations. Specifically, at temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multilayer parallel beta-sheet structure. This structure has an interstrand distance of 4.8 A and an intersheet distance of 10 A, which agree with experimental observations. Our model explains these results as follows: hydrogen-bond interactions give rise to the interstrand spacing in beta sheets, while Gō interactions between side chains make beta strands parallel to each other and allow beta sheets to pack into layers. An important feature of our results is that the aggregates contain free edges, which may allow for further aggregation of model peptides to form elongated fibrils.

Poisson-Boltzmann theory of the charge-induced adsorption of semi-flexible polyelectrolytes.

A model is suggested for the structure of an adsorbed layer of a highly charged semi-flexible polyelectrolyte on a weakly charged surface of opposite charge sign. The adsorbed phase is thin, owing to the effective reversal of the charge sign of the surface upon adsorption, and ordered, owing to the high surface density of polyelectrolyte strands caused by the generally strong binding between polyelectrolyte and surface. The Poisson-Boltzmann equation for the electrostatic interaction between the array of adsorbed polyelectrolytes and the charged surface is solved for a cylindrical geometry, both numerically, using a finite element method, and analytically within the weak curvature limit under the assumption of excess monovalent salt. For small separations, repulsive surface polarization and counterion osmotic pressure effects dominate over the electrostatic attraction and the resulting electrostatic interaction curve shows a minimum at nonzero separations on the Angstrom scale. The equilibrium density of the adsorbed phase is obtained by minimizing the total free energy under the condition of equality of chemical potential and osmotic pressure of the polyelectrolyte in solution and in the adsorbed phase. For a wide range of ionic conditions and charge densities of the charged surface, the interstrand separation as predicted by the Poisson-Boltzmann model and the analytical theory closely agree. For low to moderate charge densities of the adsorbing surface, the interstrand spacing decreases as a function of the charge density of the charged surface. Above about 0.1 M excess monovalent salt, it is only weakly dependent on the ionic strength. At high charge densities of the adsorbing surface, the interstrand spacing increases with increasing ionic strength, in line with the experiments by Fang and Yang [J. Phys. Chem. B 101, 441 (1997)].

PLASMOLYSIS, HECHTIAN STRAND FORMATION, AND LOCALIZED MEMBRANE‐WALL ADHESIONS IN THE DESMID, CLOSTERIUM ACEROSUM (CHLOROPHYTA)1

Closterium acerosum Ehrenberg (Chlorophyta) produced a distinct network of thin cytoplasmic strands, or Hechtian strands, upon controlled plasmolysis in a sucrose solution. The strands persisted for 30 min or longer and could be visualized with both LM and EM. Near the plasma membrane of the polar zones of plasmolyzing protoplasts, the strands formed a “lattice”‐like arrangement with interstrand spacing of 120–130 nm. The strands terminated at the fibrous zone of the inner cell wall stratum. Although actin cables could be found attached to the plasma membrane upon rhodamine phalloidin labeling of membrane ghosts, neither microfilaments nor microtubules were found in Hechtian strands at any stage of development. The formation of strands was not disrupted by centrifugation at 8000 g or by repeated cycles of plasmolysis‐deplasmolysis. Application of microtubule‐ or microfilament‐affecting agents or various proteolytic/polysaccharide‐degrading enzymes did not disrupt the formation of strands. Cold treatment of cells resulted in the formation of Hechtian strands.

Amyloid formation of native folded protein induced by peptide-based graft copolymer

We report here that a native folded holo-myoglobin, when incubated with a synthetic amyloidogenic peptide in aqueous solutions, forms fibrils. These fibrils took a cross-β form (inter-strand spacing: 4.65 Å and inter-sheet spacing: 10.65 Å) and bound the amyloidophilic dye Congo red as did the authentic amyloid fibrils. In contrast such fibril formation of myoglobin did not occur in the absence of the peptide. These results suggest the possibility that inter-molecular interaction of native protein with the amyloidogenic peptide trigger the amyloid formation even for the non-pathogenic native protein like myoglobin, which itself exists as a globular form, under certain conditions.

The reversible condensation and expansion of the rotavirus genome.

Understanding the structural organization of the genome is particularly relevant in segmented double-stranded RNA viruses, which exhibit endogenous transcription activity. These viruses are molecular machines capable of repeated cycles of transcription within the intact capsid. Rotavirus, a major cause of infantile gastroenteritis, is a prototypical segmented double-stranded RNA virus. From our three-dimensional structural analyses of rotavirus examined under various chemical conditions using electron cryomicroscopy, we show here that the viral genome exhibits a remarkable conformational flexibility by reversibly changing its packaging density. In the presence of ammonium ions at high pH, the genome condenses to a radius of approximately 180 A from approximately 220 A. Upon returning to physiological conditions, the genome re-expands and fully maintains its transcriptional properties. These studies provide further insights into the genome organization and suggest that the observed isometric and concentric nature of the condensation is due to strong interactions between the genome core and the transcription enzymes anchored to the capsid inner surface. The ability of the genome to condense beyond what is normally observed in the native virus indicates that the negative charges on the RNA in the native state may be only partially neutralized. Partial neutralization may be required to maintain appropriate interstrand spacing for templates to move around the enzyme complexes during transcription. Genome condensation was not observed either with increased cation concentrations at normal pH or at high pH without ammonium ions. This finding indicates that the observed genome condensation is a synergistic effect of hydroxyl and ammonium ions involving disruption of protein-RNA interactions that perhaps facilitate further charge neutralization and consequent reduction in the interstrand spacing.

Amyloid protofilament formation of hen egg lysozyme in highly concentrated ethanol solution.

Mutant human lysozymes (Ile56Thr & Asp67His) have been reported to form amyloid deposits in the viscera. From the standpoint of understanding the mechanism of amyloid formation, we searched for conditions of amyloid formation in vitro using hen egg lysozyme, which has been extensively studied from a physicochemical standpoint. It was found that the circular dichroism spectra in the far-ultraviolet region of the hen egg lysozyme changed to those characteristic of a beta-structure from the native alpha-helix rich spectrum in 90% ethanol solution. When the concentration of protein was increased to 10 mg/mL, the protein solution formed a gel in the presence of 90% ethanol, and precipitated on further addition of 10 mM NaCl. The precipitates were examined by electron microscopy, their ability to bind Congo red, and X-ray diffraction to determine whether amyloid fibrils were formed in the precipitates. Electron micrographs displayed unbranched protofilament with a diameter of approximately 70 A. The peak point of the difference spectrum for the Congo red binding assay was 541 nm, which is characteristic of amyloid fibrils. The X-ray diffraction pattern showed a sharp and intense diffraction ring at 4.7 A, a reflection that arises from the interstrand spacing in beta-sheets. These results indicate that the precipitates of hen egg lysozyme are amyloid protofilament, and that the amyloid protofilament formation of hen egg lysozyme closely follows upon the destruction of the helical and tertiary structures.

Thickness and elasticity of gram-negative murein sacculi measured by atomic force microscopy.

Atomic force microscopy was used to measure the thickness of air-dried, collapsed murein sacculi from Escherichia coli K-12 and Pseudomonas aeruginosa PAO1. Air-dried sacculi from E. coli had a thickness of 3.0 nm, whereas those from P. aeruginosa were 1.5 nm thick. When rehydrated, the sacculi of both bacteria swelled to double their anhydrous thickness. Computer simulation of a section of a model single-layer peptidoglycan network in an aqueous solution with a Debye shielding length of 0.3 nm gave a mass distribution full width at half height of 2.4 nm, in essential agreement with these results. When E. coli sacculi were suspended over a narrow groove that had been etched into a silicon surface and the tip of the atomic force microscope used to depress and stretch the peptidoglycan, an elastic modulus of 2.5 x 10(7) N/m(2) was determined for hydrated sacculi; they were perfectly elastic, springing back to their original position when the tip was removed. Dried sacculi were more rigid with a modulus of 3 x 10(8) to 4 x 10(8) N/m(2) and at times could be broken by the atomic force microscope tip. Sacculi aligned over the groove with their long axis at right angles to the channel axis were more deformable than those with their long axis parallel to the groove axis, as would be expected if the peptidoglycan strands in the sacculus were oriented at right angles to the long cell axis of this gram-negative rod. Polar caps were not found to be more rigid structures but collapsed to the same thickness as the cylindrical portions of the sacculi. The elasticity of intact E. coli sacculi is such that, if the peptidoglycan strands are aligned in unison, the interstrand spacing should increase by 12% with every 1 atm increase in (turgor) pressure. Assuming an unstressed hydrated interstrand spacing of 1.3 nm (R. E. Burge, A. G. Fowler, and D. A. Reaveley, J. Mol. Biol. 117:927-953, 1977) and an internal turgor pressure of 3 to 5 atm (or 304 to 507 kPa) (A. L. Koch, Adv. Microbial Physiol. 24:301-366, 1983), the natural interstrand spacing in cells would be 1.6 to 2.0 nm. Clearly, if large macromolecules of a diameter greater than these spacings are secreted through this layer, the local ordering of the peptidoglycan must somehow be disrupted.

Three-Dimensional Structure of HIV-1 Rev Protein Filaments

The HIV-1 Rev protein facilitates the export of incompletely spliced and unspliced viral mRNAs from the nucleus. Rev polymerizes into two types of filamentsin vitro. In the presence of RNA, Rev forms poorly ordered structures, while in the absence of RNA it polymerizes into regular hollow filaments. We have determined the helical structure of the latter filaments by analysis of cryo-electron micrographs, taking into account STEM measurements of mass-per-unit-length. They are made up of Rev dimers, arranged in a six-start helix, with 31 dimers in 2 turns, a pitch angle of 45°, and an interstrand spacing of 3.8 nm. Three-dimensional reconstruction at 2.1 nm resolution reveals a smooth outer surface and a featured inner surface, with outer and inner diameters of ≈14.8 and ≈10.4 nm, respectively. The Rev dimer has a “top-hat” shape with a cylinder ≈3.2 nm in diameter and ≈2.2 nm high, pointing inward: the thinner rim areas pack together to form the filament wall. Raman spectroscopy shows polymerized Rev to have ≈54% α-helix and 20–24% β-sheet content. Electron microdiffraction of aligned filaments reveals a broad meridional reflection at ≈(0.51 nm)−1, suggesting approximate alignment of the α-helices with the filament axis. Based on these data, a molecular model for the Rev filament is proposed.

Anchor field tests in carboniferous strata

The paper discusses the preliminary findings of full scale tests on 57 anchors installed in carboniferous sediments. The site geology is briefly described together with the anchor construction and testing methods adopted. To investigate the influence of anchor geometry on failure mode, anchors ranging in overall depth from 0.75 to 12 metres were tested with grouted fixed anchor lengths of 0.75 to 6 metres. The observed effects of depth of embedment, grout surcharge, tendon configuration, interstrand spacing and tendon density on anchor performance are discussed in relation to current practice. Measurements of interfacial bond and load transmission are presented.