Imaging studies of peripheral nerve regeneration induced by porous collagen biomaterials

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2013.Cataloged from PDF version of thesis.Includes bibliographical references.There is urgent need to develop treatments for inducing regeneration in injured organs. Porous collagen-based scaffolds have been utilized clinically to induce regeneration in skin and peripheral nerves, however still there is no complete explanation about the underlying mechanism. This thesis utilizes advanced microscopy to study the expression of contractile cell phenotypes during wound healing, a phenotype believed to affect significantly the final outcome. The first part develops an efficient pipeline for processing challenging spectral fluorescence microscopy images. Images are segmented into regions of objects by refining the outcome of a pixel-wide model selection classifier by an efficient Markov Random Field model. The methods of this part are utilized by the following parts. The second part extends the image informatics methodology in studying signal transduction networks in cells interacting with 3D matrices. The methodology is applied in a pilot study of TGFP signal transduction by the SMAD pathway in fibroblasts seeded in porous collagen scaffolds. Preliminary analysis suggests that the differential effect of TGFP1 and TGFP3 to cells could be attributed to the "non-canonical" SMADI and SMAD5. The third part is an ex vivo imaging study of peripheral nerve regeneration, which focuses on the formation of a capsule of contractile cells around transected rat sciatic nerves grafted with collagen scaffolds, 1 or 2 weeks post-injury. It follows a recent study that highlights an inverse relationship between the quality of the newly formed nerve tissue and the size of the contractile cell capsule 9 weeks post-injury. Results suggest that "active" biomaterials result in significantly thinner capsule already 1 week post-injury. The fourth part describes a novel method for quantifying the surface chemistry of 3D matrices. The method is an in situ binding assay that utilizes fluorescently labeled recombinant proteins that emulate the receptor of , and is applied to quantify the density of ligands for integrins a113, a2p1 on the surface of porous collagen scaffolds. Results provide estimates for the density of ligands on "active" and "inactive" scaffolds and demonstrate that chemical crosslinking can affect the surface chemistry of biomaterials, therefore can affect the way cells sense and respond to the material.by Dimitrios S. Tzeranis.Ph. D

Quantifying the Dynamics of Bacterial Secondary Metabolites by Spectral Multiphoton Microscopy

Phenazines, a group of fluorescent small molecules produced by the bacterium Pseudomonas aeruginosa, play a role in maintaining cellular redox homeostasis. Phenazines have been challenging to study in vivo due to their redox activity, presence both intra- and extracellularly, and their diverse chemical properties. Here, we describe a noninvasive in vivo optical technique to monitor phenazine concentrations within bacterial cells using time-lapsed spectral multiphoton fluorescence microscopy. This technique enables simultaneous monitoring of multiple weakly fluorescent molecules (phenazines, siderophores, NAD(P)H) expressed by bacteria in culture. This work provides the first in vivo measurements of reduced phenazine concentration as well as the first description of the temporal dynamics of the phenazine-NAD(P)H redox system in Pseudomonas aeruginosa, illuminating an unanticipated role for 1-hydroxyphenazine. Similar approaches could be used to study the abundance and redox dynamics of a wide range of small molecules within bacteria, both as single cells and in communities

Regeneration of injured skin and peripheral nerves requires control of wound contraction, not scar formation

We review the mounting evidence that regeneration is induced in wounds in skin and peripheral nerves by a simple modification of the wound healing process. Here, the process of induced regeneration is compared to the other two well-known processes by which wounds close, i.e., contraction and scar formation. Direct evidence supports the hypothesis that the mechanical force of contraction (planar in skin wounds, circumferential in nerve wounds) is the driver guiding the orientation of assemblies of myofibroblasts (MFB) and collagen fibers during scar formation in untreated wounds. We conclude that scar formation depends critically on wound contraction and is, therefore, a healing process secondary to contraction. Wound contraction and regeneration did not coincide during healing in a number of experimental models of spontaneous (untreated) regeneration described in the literature. Furthermore, in other studies in which an efficient contraction-blocker, a collagen scaffold named dermis regeneration template (DRT), and variants of it, were grafted on skin wounds or peripheral nerve wounds, regeneration was systematically observed in the absence of contraction. We conclude that contraction and regeneration are mutually antagonistic processes. A dramatic change in the phenotype of MFB was observed when the contraction-blocking scaffold DRT was used to treat wounds in skin and peripheral nerves. The phenotype change was directly observed as drastic reduction in MFB density, dispersion of MFB assemblies and loss of alignment of the long MFB axes. These observations were explained by the evidence of a surface-biological interaction of MFB with the scaffold, specifically involving binding of MFB integrins α[subscript 1]β[subscript 1] and α[subscript 2]β[subscript 1] to ligands GFOGER and GLOGER naturally present on the surface of the collagen scaffold. In summary, we show that regeneration of wounded skin and peripheral nerves in the adult mammal can be induced simply by appropriate control of wound contraction, rather than of scar formation.National Institutes of Health (U.S.) (Grant RO1 NS051320)National Institutes of Health (U.S.) (Grant 5‐P41‐EB015871‐28)Horizon 2020 Framework Programme (European Commission) (Grant DLV‐658850)Singapore-MIT Alliance for Research and Technology (SMART) (Grant 5‐P41‐EB015871‐28)Hamamatsu Corporatio

Manipulation of flexible structural modules by space robots during LSS construction

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2005.Includes bibliographical references (leaves 86-90).Future space structures are expected to have very large size. Such Large Space Structures (LSS) will be constructed in-orbit, probably by assembling large structural modules. This is a dangerous and difficult task for humans. On the other hand, this is a challenging and promising application for space robotics. This work provides a planning and control architecture for the manipulation of a large flexible structural module in the proximity of the LSS, by a team of space manipulators that are mounted on the LSS. In this task, the payload (module) and the base structure (LSS) of the robots are assumed to be very compliant. Interface forces between robots and flexible structures induce undesirable vibration. The approach developed here is to plan and control the forces that robots apply to the flexible structures so that they maneuver the module precisely while exciting low levels of residual vibration in the module and the LSS. Robot use different control implementations to control the forces they apply to different kinds of flexible structures. Robots plan and control cooperatively the forces they apply to the module.(cont.) Each robot exploits its redundancy to minimize the base reaction forces it applies to the LSS and to avoid undesirable configurations. Simulation results demonstrate the effectiveness of the developed architecture in positioning the module precisely and exciting low levels of residual vibration in the module and the LSS.by Dimitrios Spyridon Tzeranis.S.M

Quantifying the surface chemistry of 3D matrices in situ

Despite the major role of the matrix (the insoluble environment around cells) in physiology and pathology, there are very few and limited methods that can quantify the surface chemistry of a 3D matrix such as a biomaterial or tissue ECM. This study describes a novel optical-based methodology that can quantify the surface chemistry (density of adhesion ligands for particular cell adhesion receptors) of a matrix in situ. The methodology utilizes fluorescent analogs (markers) of the receptor of interest and a series of binding assays, where the amount of bound markers on the matrix is quantified via spectral multi-photon imaging. The study provides preliminary results for the quantification of the ligands for the two major collagen-binding integrins (α[subscript 1]β[subscript 1], α[subscript 2]β[subscript 1]) in porous collagen scaffolds that have been shown to be able to induce maximum regeneration in transected peripheral nerves. The developed methodology opens the way for quantitative descriptions of the insoluble microenvironment of cells in physiology and pathology, and for integrating the matrix in quantitative models of cell signaling.National Institutes of Health (U.S.) (RO1 NS051320)Singapore-MIT Alliance for Research and Technolog

In Situ Quantification of Surface Chemistry in Porous Collagen Biomaterials

Cells inside a 3D matrix (such as tissue extracellular matrix or biomaterials) sense their insoluble environment through specific binding interactions between their adhesion receptors and ligands present on the matrix surface. Despite the critical role of the insoluble matrix in cell regulation, there exist no widely-applicable methods for quantifying the chemical stimuli provided by a matrix to cells. Here, we describe a general-purpose technique for quantifying in situ the density of ligands for specific cell adhesion receptors of interest on the surface of a 3D matrix. This paper improves significantly the accuracy of the procedure introduced in a previous publication by detailed marker characterization, optimized staining, and improved data interpretation. The optimized methodology is utilized to quantify the ligands of integrins α[subscript 1]β[subscript 1], α[subscript 2]β[subscript 1] on two kinds of matched porous collagen scaffolds, which are shown to possess significantly different ligand density, and significantly different ability to induce peripheral nerve regeneration in vivo. Data support the hypothesis that cell adhesion regulates contractile cell phenotypes, recently shown to be inversely related to organ regeneration. The technique provides a standardized way to quantify the surface chemistry of 3D matrices, and a means for introducing matrix effects in quantitative biological models.National Institutes of Health (U.S.) (Grant RO1 NS051320)National Institutes of Health. National Institute for Biomedical Imaging and Bioengineering (Biomechanics Training Grant T32EB006348)National Science Foundation (U.S.). Graduate Research Fellowship Program (Grant DGE-1122374)Singapore-MIT Alliance for Research and Technology (SMART). BioSym IRGComputation and Systems Biology Programme of Singapore--Massachusetts Institute of Technology AllianceNational Institutes of Health (U.S.) (Grant 9P41EB015871-26A1

Image informatics for studying signal transduction in cells interacting with 3D matrices

Cells sense and respond to chemical stimuli on their environment via signal transduction pathways, complex networks of proteins whose interactions transmit chemical information. This work describes an implementation of image informatics, imaging-based methodologies for studying signal transduction networks. The methodology developed focuses on studying signal transduction networks in cells that interact with 3D matrices. It utilizes shRNA-based knock down of network components, 3D high-content imaging of cells inside the matrix by spectral multi-photon microscopy, and single-cell quantification using features that describe both cell morphology and cell-matrix adhesion pattern. The methodology is applied in a pilot study of TGFβ signaling via the SMAD pathway in fibroblasts cultured inside porous collagen-GAG scaffolds, biomaterials similar to the ones used clinically to induce skin regeneration. Preliminary results suggest that knocking down all rSMAD components affects fibroblast response to TGFβ1 and TGFβ3 isoforms in different ways, and suggest a potential role for SMAD1 and SMAD5 in regulating TGFβ isoform response. These preliminary results need to be verified with proteomic results that can provide solid evidence about the particular role of individual components of the SMAD pathway.National Institutes of Health (U.S.) (RO1 NS051320)Singapore-MIT Alliance for Research and Technolog

Changes in the biochemical constituents and morphologic appearance of the human cervical stroma during pregnancy

Objective: The cervix is the lower portion of the uterus. It is composed of fibrous tissue and its mechanical integrity is crucial for maintaining a healthy gestation. During normal pregnancy, the cervical extracellular matrix (ECM) remodels in preparation for labor. The objective of this study was to investigate the biochemical and morphological changes in cervical stroma associated with physiological remodeling during normal pregnancy. Study design: Using human cervical tissue obtained from pregnant and non-pregnant patients, the ECM was analyzed for its biochemical constituents and histologic morphology. The ECM was assayed for hydration, collagen concentration, collagen solubility, total sulfated glycosaminoglycan concentration, and individual disaccharide concentration. The ECM morphology was visualized using conventional histological techniques (Masson's trichrome stain, polarized light microscopy) as well as second harmonic generation (SHG) imaging. Results: When comparing pregnant to non-pregnant tissue, significant increases were measured for total sulfated glycosaminoglycans, hyaluronic acid, and collagen solubility. The microscopy studies confirmed that the collagenous network of the cervical stroma was anisotropic and pregnancy was associated with a discernable decrease in collagen organization. Conclusion: Significant changes were seen in the concentration and organization of cervical ECM constituents during normal pregnancy