Fine-tuning of substrate architecture and surface chemistry promotes muscle tissue development

Tissue engineering has been increasingly brought to the scientific spotlight in response to the tremendous demand for regeneration, restoration or substitution of skeletal or cardiac muscle after traumatic injury, tumour ablation or myocardial infarction. In vitro generation of a highly organized and contractile muscle tissue, however, crucially depends on an appropriate design of the cell culture substrate. The present work evaluated the impact of substrate properties, in particular morphology, chemical surface composition and mechanical properties, on muscle cell fate. To this end, aligned and randomly oriented micron (3.3±0.8 μm) or nano (237±98 nm) scaled fibrous poly(ε-caprolactone) non-wovens were processed by electrospinning. A nanometer-thick oxygen functional hydrocarbon coating was deposited by a radio frequency plasma process. C2C12 muscle cells were grown on pure and as-functionalized substrates and analysed for viability, proliferation, spatial orientation, differentiation and contractility. Cell orientation has been shown to depend strongly on substrate architecture, being most pronounced on micron-scaled parallel-oriented fibres. Oxygen functional hydrocarbons, representing stable, non-immunogenic surface groups, were identified as strong triggers for myotube differentiation. Accordingly, the highest myotube density (28±15% of total substrate area), sarcomeric striation and contractility were found on plasma-coated substrates. The current study highlights the manifold material characteristics to be addressed during the substrate design process and provides insight into processes to improve bio-interfaces.

Characterization of vascular cavity coatings and microscopic tube-shaped structures from Upper Cretaceous dinosaur bone: evidence of a bacterial origin for dinosaur blood vessels""

Recent claims of blood vessels extracted from dinosaur fossils challenge classical views of soft-tissue preservation. Alternatively, these structures may represent postdepositional,diagenetic biofilms that grew on vascular cavity surfaces within the fossil. Similar red, hollow, tube-shaped structures were recovered from well-preserved and poorly-preserved (abraded, desiccated, exposed) Upper Cretaceous dinosaur fossils in this study. Integration of light microscopy, scanning electron microscopy, and energy dispersive x-ray spectroscopy was used to compare these vessel structures to the fossils from which they are derived. Vessel structures are typically 100-400 μm long, 0.5-1.5 μm thick, 10-40 μm in diameter and take on a wide range of straight, curved, andbranching morphologies. Interior surfaces vary from smooth to globular and typically contain spheres, rods, and fibrous structures (< 2 μm in diameter) incorporated into the surface. Exterior surfaces exhibit 2-μm-tall converging ridges, spaced 1-3 μm apart, that are sub-parallel to the long axis of the vessel structure. Fossil vascular cavities are typically coated with a smooth or grainy orange layer that shows a wide range of textures including smooth, globular, rough, ropy, and combinations thereof. Coatings tend to overlay secondary mineral crystals and framboids, confirming they are not primary structures of the fossil. For some cavity coatings, the surface that had been in contact with the bone exhibits a ridged texture, similar to that of vessel structures, having formed as a mold of the intravascular bone surface. Thus, vessel structures are interpreted as intact cavity coatings isolated after the fossil is demineralized. The presence of framboids and structures consistent in size and shape with bacteria cells, the abundance of iron in cavity coatings, and the growth of biofilms directly from the fossil that resemble respective cavity coatings support the hypothesis that vessel structures result from ironconsuming bacteria that form biofilms on the intravascular bone surfaces of fossil dinosaur bone. This also accounts for microstructures resembling osteocytes as some fossil lacunae are filled with the same iron oxide that comprises vessel structures andcoatings. Results of this study show that systematic, high-resolution SEM analyses of vertebrate fossils can provide improved insight on microtaphonomic processes, including the role of bacteria in diagenesis. These results conflict with earlier claims of dinosaurblood vessels and osteocytes.

Fabrication of cone-shaped boron doped diamond and gold nanoelectrodes for AFM-SECM

We demonstrate a reliable microfabrication process for a combined atomic force microscopy (AFM) and scanning electrochemical microscopy (SECM) measurement tool. Integrated cone-shaped sensors with boron doped diamond (BDD) or gold (Au) electrodes were fabricated from commercially available AFM probes. The sensor formation process is based on mature semiconductor processing techniques, including focused ion beam (FIB) machining, and highly selective reactive ion etching (RIE). The fabrication approach preserves the geometry of the original AFM tips resulting in well reproducible nanoscaled sensors. The feasibility and functionality of the fully featured tips are demonstrated by cyclic voltammetry, showing good agreement between the measured and calculated currents of the cone-shaped AFM-SECM electrodes.

Performance Tuning Non-Uniform Sampling for Sensitivity Enhancement of Signal-Limited Biological NMR

Non-uniform sampling (NUS) has been established as a route to obtaining true sensitivity enhancements when recording indirect dimensions of decaying signals in the same total experimental time as traditional uniform incrementation of the indirect evolution period. Theory and experiments have shown that NUS can yield up to two-fold improvements in the intrinsic signal-to-noise ratio (SNR) of each dimension, while even conservative protocols can yield 20-40 % improvements in the intrinsic SNR of NMR data. Applications of biological NMR that can benefit from these improvements are emerging, and in this work we develop some practical aspects of applying NUS nD-NMR to studies that approach the traditional detection limit of nD-NMR spectroscopy. Conditions for obtaining high NUS sensitivity enhancements are considered here in the context of enabling H-1,N-15-HSQC experiments on natural abundance protein samples and H-1,C-13-HMBC experiments on a challenging natural product. Through systematic studies we arrive at more precise guidelines to contrast sensitivity enhancements with reduced line shape constraints, and report an alternative sampling density based on a quarter-wave sinusoidal distribution that returns the highest fidelity we have seen to date in line shapes obtained by maximum entropy processing of non-uniformly sampled data.

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Design of custom-shaped vascularized tissues using microtissue spheroids as minimal building units

Tissue engineering strategies are gathering clinical momentum in regenerative medicine and are expected to provide excellent opportunities for therapy for difficult-to-treat human pathologies. Being aware of the requirement to produce larger artificial tissue implants for clinical applications, we used microtissues, produced using gravity-enforced self-assembly of monodispersed primary cells, as minimal tissue units to generate scaffold-free vascularized artificial macrotissues in custom-shaped agarose molds. Mouse myoblast, pig and human articular-derived chondrocytes, and human myofibroblast (HMF)-composed microtissues (microm3 scale) were amalgamated to form coherent macrotissue patches (mm3 scale) of a desired shape. Macrotissues, assembled from the human umbilical vein endothelial cell (HUVEC)-coated HMF microtissues, developed a vascular system, which functionally connected to the chicken embryo's vasculature after implantation. The design of scaffold-free vascularized macrotissues is a first step toward the scale-up and production of artificial tissue implants for future tissue engineering initiatives.

Biological materials : Part A. tuning LCST of raft copolymers and gold/copolymer hybrid nanoparticles and Part B. biobased nanomaterials

The research described in this dissertation is comprised of two major parts. The first part studied the effects of asymmetric amphiphilic end groups on the thermo-response of diblock copolymers of (oligo/di(ethylene glycol) methyl ether (meth)acrylates, OEGA/DEGMA) and the hybrid nanoparticles of these copolymers with a gold nanoparticle core. Placing the more hydrophilic end group on the more hydrophilic block significantly increased the cloud point compared to a similar copolymer composition with the end group placement reversed. For a given composition, the cloud point was shifted by as much as 28 °C depending on the placement of end groups. This is a much stronger effect than either changing the hydrophilic/hydrophobic block ratio or replacing the hydrophilic acrylate monomer with the equivalent methacrylate monomer. The temperature range of the coil-globule transition was also altered. Binding these diblock copolymers to a gold core decreased the cloud point by 5-15 °C and narrowed the temperature range of the coil-globule transition. The effects were more pronounced when the gold core was bound to the less hydrophilic block. Given the limited numbers of monomers that are approved safe for in vivo use, employing amphiphilic end group placement is a useful tool to tune a thermo-response without otherwise changing the copolymer composition. The second part of the dissertation investigated the production of value-added nanomaterials from two biorefinery “wastes”: lignin and peptidoglycan. Different solvents and spinning methods (melt-, wet-, and electro-spinning) were tested to make lignin/cellulose blended and carbonized fibers. Only electro-spinning yielded fibers having a small enough diameter for efficient carbonization ( Peptidoglycan (a bacterial cell wall material) was copolymerized with poly-(3-hydroxybutyrate), a common polyhydroxyalkanoate produced by bacteria with the objective of determining if a useful material could be obtained with a less rigorous work-up on harvesting polyhydroxyalkanoates. The copolyesteramide product having 25 wt.% peptidoglycan from a highly purified peptidoglycan increased thermal stability by 100-200 °C compared to the poly-(3-hydroxybutyrate) control, while a less pure peptidoglycan, harvested from B. megaterium (ATCC 11561), gave a 25-50 °C increase in thermal stability. Both copolymers absorbed more moisture than pure poly-(3-hydroxybutyrate). The results suggest that a less rigorously harvested and purified polyhydroxyalkanoate might be useful for some applications.

TUNING, AVO, AND FLAT-SPOT EFFECTS IN A SEISMIC ANALYSIS OF NORTH SEA BLOCK F3

Reflection seismic data from the F3 block in the Dutch North Sea exhibits many large-amplitude reflections at shallow horizons, typically categorized as “brightspots ” (Schroot and Schuttenhelm, 2003), mainly because of their bright appearance. In most cases, these bright reflections show a significant “flatness” contrasting with local structural trends. While flatspots are often easily identified in thick reservoirs, we have often occasionally observed apparent flatspot tuning effects at fluid contacts near reservoir edges and in thin reservoir beds, while only poorly understanding them. We conclude that many of the shallow large-amplitude reflections in block F3 are dominated by flatspots, and we investigate the thin-bed tuning effects that such flatspots cause as they interact with the reflection from the reservoir’s upper boundary. There are two possible effects to be considered: (1) the “wedge-model” tuning effects of the flatspot and overlying brightspots, dimspots, or polarity-reversals; and (2) the stacking effects that result from possible inclusion of post-critical flatspot reflections in these shallow sands. We modeled the effects of these two phenomena for the particular stratigraphic sequence in block F3. Our results suggest that stacking of post-critical flatspot reflections can cause similar large-amplitude but flat reflections, in some cases even causing an interface expected to produce a ‘dimspot’ to appear as a ‘brightspot’. Analysis of NMO stretch and muting shows the likely exclusion of critical offset data in stacked output. If post-critical reflections are included in stacking, unusual results will be observed. In the North Sea case, we conclude the tuning effect was the primary reason causing for the brightness and flatness of these reflections. However, it is still important to note that care should be taken while applying muting on reflections with wide range of incidence angles and the inclusion of critical offset data may cause some spurious features in the stacked section.