The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey partial differential equation. Under the assumption of negligible water exchange between compartments, the time-dependent apparent diffusion coefficient can be directly computed from the solution of a diffusion equation subject to a time-dependent Neumann boundary condition. This paper describes a publicly available MATLAB toolbox called SpinDoctor that can be used 1) to solve the Bloch-Torrey partial differential equation in order to simulate the diffusion magnetic resonance imaging signal; 2) to solve a diffusion partial differential equation to obtain directly the apparent diffusion coefficient; 3) to compare the simulated apparent diffusion coefficient with a short-time approximation formula. The partial differential equations are solved by P1 finite elements combined with built-in MATLAB routines for solving ordinary differential equations. The finite element mesh generation is performed using an external package called Tetgen. SpinDoctor provides built-in options of including 1) spherical cells with a nucleus; 2) cylindrical cells with a myelin layer; 3) an extra-cellular space enclosed either a) in a box or b) in a tight wrapping around the cells; 4) deformation of canonical cells by bending and twisting; 5) permeable membranes; Built-in diffusion-encoding pulse sequences include the Pulsed Gradient Spin Echo and the Oscillating Gradient Spin Echo. We describe in detail how to use the SpinDoctor toolbox. We validate SpinDoctor simulations using reference signals computed by the Matrix Formalism method. We compare the accuracy and computational time of SpinDoctor simulations with Monte-Carlo simulations and show significant speed-up of SpinDoctor over Monte-Carlo simulations in complex geometries. We also illustrate several extensions of SpinDoctor functionalities, including the incorporation of T2 relaxation, the simulation of non-standard diffusion-encoding sequences, as well as the use of externally generated geometrical meshes.
- Keywords
- Apparent diffusion coefficient, Bloch-torrey equation, Diffusion magnetic resonance imaging, Finite elements, Simulation,
- MeSH
- Diffusion Magnetic Resonance Imaging methods MeSH
- Humans MeSH
- Brain * MeSH
- Neuroimaging methods MeSH
- Computer Simulation MeSH
- Software * MeSH
- Models, Theoretical * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Keywords
- ECM, cell biology, extra cellular matrix, mechanical and topographical cues, physico-chemical parameter, scaffold matrix,
- Publication type
- Editorial MeSH
SIGNIFICANCE: Mitochondria are the energetic, metabolic, redox, and information signaling centers of the cell. Substrate pressure, mitochondrial network dynamics, and cristae morphology state are integrated by the protonmotive force Δp or its potential component, ΔΨ, which are attenuated by proton backflux into the matrix, termed uncoupling. The mitochondrial uncoupling proteins (UCP1-5) play an eminent role in the regulation of each of the mentioned aspects, being involved in numerous physiological events including redox signaling. Recent Advances: UCP2 structure, including purine nucleotide and fatty acid (FA) binding sites, strongly support the FA cycling mechanism: UCP2 expels FA anions, whereas uncoupling is achieved by the membrane backflux of protonated FA. Nascent FAs, cleaved by phospholipases, are preferential. The resulting Δp dissipation decreases superoxide formation dependent on Δp. UCP-mediated antioxidant protection and its impairment are expected to play a major role in cell physiology and pathology. Moreover, UCP2-mediated aspartate, oxaloacetate, and malate antiport with phosphate is expected to alter metabolism of cancer cells. CRITICAL ISSUES: A wide range of UCP antioxidant effects and participations in redox signaling have been reported; however, mechanisms of UCP activation are still debated. Switching off/on the UCP2 protonophoretic function might serve as redox signaling either by employing/releasing the extra capacity of cell antioxidant systems or by directly increasing/decreasing mitochondrial superoxide sources. Rapid UCP2 degradation, FA levels, elevation of purine nucleotides, decreased Mg2+, or increased pyruvate accumulation may initiate UCP-mediated redox signaling. FUTURE DIRECTIONS: Issues such as UCP2 participation in glucose sensing, neuronal (synaptic) function, and immune cell activation should be elucidated. Antioxid. Redox Signal. 29, 667-714.
- Keywords
- UCP2, anion transport, attenuation of superoxide formation, fatty acid cycling, mitochondrial uncoupling proteins, redox signaling,
- MeSH
- Antioxidants metabolism MeSH
- Humans MeSH
- Mitochondrial Uncoupling Proteins metabolism MeSH
- Oxidation-Reduction MeSH
- Signal Transduction * MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Names of Substances
- Antioxidants MeSH
- Mitochondrial Uncoupling Proteins MeSH
The cutis laxa syndromes are multisystem disorders that share loose redundant inelastic and wrinkled skin as a common hallmark clinical feature. The underlying molecular defects are heterogeneous and 13 different genes have been involved until now, all of them being implicated in elastic fiber assembly. We provide here molecular and clinical characterization of three unrelated patients with a very rare phenotype associating cutis laxa, facial dysmorphism, severe growth retardation, hyperostotic skeletal dysplasia, and intellectual disability. This disorder called Lenz-Majewski syndrome (LMS) is associated with gain of function mutations in PTDSS1, encoding an enzyme involved in phospholipid biosynthesis. This report illustrates that LMS is an unequivocal cutis laxa syndrome and expands the clinical and molecular spectrum of this group of disorders. In the neonatal period, brachydactyly and facial dysmorphism are two early distinctive signs, later followed by intellectual disability and hyperostotic skeletal dysplasia with severe dwarfism allowing differentiation of this condition from other cutis laxa phenotypes. Further studies are needed to understand the link between PTDSS1 and extra cellular matrix assembly.
- Keywords
- Lenz-Majewski syndrome, PTDSS1, cutis laxa, hyperostotic skeletal dysplasia,
- MeSH
- Alleles MeSH
- Cutis Laxa diagnosis genetics MeSH
- Child MeSH
- Adult MeSH
- Exons MeSH
- Facies MeSH
- Phenotype * MeSH
- Genetic Association Studies MeSH
- Genotype MeSH
- Hyperostosis diagnosis genetics MeSH
- Humans MeSH
- Mutation * MeSH
- Child, Preschool MeSH
- Radiography MeSH
- Nitrogenous Group Transferases genetics MeSH
- Check Tag
- Child MeSH
- Adult MeSH
- Humans MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Names of Substances
- phospholipid serine base exchange enzyme MeSH Browser
- Nitrogenous Group Transferases MeSH
Ameloblastin (AMBN), an important component of the self-assembled enamel extra cellular matrix, contains several in silico predicted phosphorylation sites. However, to what extent these sites actually are phosphorylated and the possible effects of such post-translational modifications are still largely unknown. Here we report on in vitro experiments aimed at investigating what sites in AMBN are phosphorylated by casein kinase 2 (CK2) and protein kinase A (PKA) and the impact such phosphorylation has on self-assembly and calcium binding. All predicted sites in AMBN can be phosphorylated by CK2 and/or PKA. The experiments show that phosphorylation, especially in the exon 5 derived part of the molecule, is inversely correlated with AMBN self-assembly. These results support earlier findings suggesting that AMBN self-assembly is mostly dependent on the exon 5 encoded region of the AMBN gene. Phosphorylation was significantly more efficient when the AMBN molecules were in solution and not present as supramolecular assemblies, suggesting that post-translational modification of AMBN must take place before the enamel matrix molecules self-assemble inside the ameloblast cell. Moreover, phosphorylation of exon 5, and the consequent reduction in self-assembly, seem to reduce the calcium binding capacity of AMBN suggesting that post-translational modification of AMBN also can be involved in control of free Ca2+ during enamel extra cellular matrix biomineralization. Finally, it is speculated that phosphorylation can provide a functional crossroad for AMBN either to be phosphorylated and act as monomeric signal molecule during early odontogenesis and bone formation, or escape phosphorylation to be subsequently secreted as supramolecular assemblies that partake in enamel matrix structure and mineralization.
- Keywords
- Ca2+- binding, ameloblastin, casein kinase 2, enamel, intrinsically disordered proteins, phosphorylation, protein kinase A, self-assembly,
- Publication type
- Journal Article MeSH
INTRODUCTION: Remodeling of human placental membranes (amniochorionic or fetalmembrane) throughout gestation, a necessity to accommodate increasing uterine volume, involves continuous alterations (replacement of cells and remodeling of extracellular matrix). Methodologic limitations have obscured microscopic determination of cellular and layer-level alterations. This study used a combination of advanced imaging by multiphoton autofluorescence microscopy (MPAM) and second harmonic generation (SHG) microscopy along with tissue optical clearing to characterize the 3Dimensional multilayer organization of placental membranes. METHODS: Placental membranes biopsies (6 mm) collected from term, not-in-labor cesarean deliveries (n = 7) were fixed in 10% formalin (native) or treated with 2,2'-thiodiethanol to render them transparent for deeper imaging. Native and cleared tissues were imaged using MPAM (cellular autofluorescence) and SHG (fibrillar collagen). Depth z-stacks captured the amnion epithelium, underlying matrix layers, and in the cleared biopsies, the decidua layer. RESULTS: MPAM and SHG revealed fetal membrane epithelial topography and collagen organization in multiple matrix layers. Term amnion layers showed epithelial shedding and gaps. Optical clearing provided full-depth imaging with improved visualization of collagen structure, mesenchymal cells in extracellular matrix layers, and decidua morphology. Layer thicknesses measured by imaging corroborated with histology. Mosaic tiling of MPAM/SHG image stacks allowed large area visualization of entire biopsies. CONCLUSION: MPAM-SHG microscopy allowed for study of this multi-layered tissue and revealed shedding, gap formation, and other structural changes. This approach could be used to study structural changes associated with membranes as well as other uterine tissues to better understand events in normal and abnormal parturition.
- Keywords
- Amniochorion, Epithelial shedding, Membrane rupture, Multiphoton microscopy, Nonlinear optical microscopy, Optical clearing, Placenta, Pregnancy and parturition, Second harmonic generation microscopy,
- MeSH
- Extracellular Matrix MeSH
- Extraembryonic Membranes anatomy & histology diagnostic imaging MeSH
- Histocytological Preparation Techniques MeSH
- Humans MeSH
- Microscopy, Fluorescence, Multiphoton * MeSH
- Second Harmonic Generation Microscopy * MeSH
- Placenta anatomy & histology diagnostic imaging MeSH
- Pregnancy MeSH
- Imaging, Three-Dimensional MeSH
- Check Tag
- Humans MeSH
- Pregnancy MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
The replacement of pancreatic islets for the possible treatment of type 1 diabetes is limited by the extremely high oxygen demand of the islets. To this end, here we hypothesize to create a novel extra-hepatic highly-vascularized bioartificial cavity using a porous scaffold as a template and using the host body as a living bioreactor for subsequent islet transplantation. Polylactide-based capsular-shaped anisotropic channeled porous scaffolds were prepared by following the unidirectional thermally-induced phase separation technique, and were implanted under the skin and in the greater omentum of Brown Norway rats. Polyamide mesh-based isotropic regular porous capsules were used as the controls. After 4weeks, the implants were excised and analyzed by histology. The hematoxylin and eosin, as well as Masson's trichrome staining, revealed a) low or no infiltration of giant inflammatory cells in the implant, b) minor but insignificant fibrosis around the implant, c) guided infiltration of host cells in the test capsule in contrast to random cell infiltration in the control capsule, and d) relatively superior cell infiltration in the capsules implanted in the greater omentum than in the capsules implanted under the skin. Furthermore, the anti-CD31 immunohistochemistry staining revealed numerous vessels at the implant site, but mostly on the external surface of the capsules. Taken together, the current study, the first of its kind, is a significant step-forward towards engineering a bioartificial microenvironment for the transplantation of islets.
- MeSH
- Anisotropy MeSH
- Platelet Endothelial Cell Adhesion Molecule-1 MeSH
- Cellular Microenvironment MeSH
- Fibrosis MeSH
- Neovascularization, Physiologic drug effects MeSH
- Polylactic Acid-Polyglycolic Acid Copolymer MeSH
- Rats MeSH
- Lactic Acid chemistry MeSH
- Polyglycolic Acid chemistry MeSH
- Islets of Langerhans * MeSH
- Porosity MeSH
- Rats, Inbred BN MeSH
- Tissue Scaffolds MeSH
- Capsules MeSH
- Islets of Langerhans Transplantation methods MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Platelet Endothelial Cell Adhesion Molecule-1 MeSH
- Polylactic Acid-Polyglycolic Acid Copolymer MeSH
- Lactic Acid MeSH
- Polyglycolic Acid MeSH
- Capsules MeSH
Turing's diffusion-driven instability for the standard two species reaction-diffusion system is only achievable under well-known and rather restrictive conditions on both the diffusion rates and the kinetic parameters, which necessitates the pairing of a self-activator with a self-inhibitor. In this study we generalize the standard two-species model by considering the case where the reactants can bind to an immobile substrate, for instance extra-cellular matrix, and investigate the influence of this dynamics on Turing's diffusion-driven instability. Such systems have been previously studied on the grounds that binding of the self-activator to a substrate may effectively reduce its diffusion rate and thus induce a Turing instability for species with equal diffusion coefficients, as originally demonstrated by Lengyel and Epstein (1992) under the assumption that the bound state dynamics occurs on a fast timescale. We, however, analyse the full system without any separation of timescales and demonstrate that the full system also allows a relaxation of the standard constraints on the reaction kinetics for the Turing instability, increasing the type of interactions that could give rise to spatial patterning. In particular, we show that two self-activators can undertake a diffusively driven instability in the presence of a binding immobile substrate, highlighting that the interactions required of a putative biological Turing instability need not be associated with a self-activator-self-inhibitor morphogen pair.
The c-ets1 proto-oncogene encodes a transcription factor that binds a GGAA/T purine rich core DNA sequence. During normal as well as pathological development, the expression of c-ets1 is associated with the occurrence of invasive processes, either in invading cells or in the invaded tissue. Cellular regulatory sequences responsive to the c-Ets1 proteins include a urokinase-type plasminogen activator (u-PA) gene enhancer, the stromelysin-1 and the collagenase-1 gene promoters. Since invasive processes are thought to require the remodeling of the extra-cellular matrix, we investigate the relationships between c-Ets1 and the expression pattern of transcripts encoding these matrix degrading proteases, in embryos and in solid tumors.
- MeSH
- Neovascularization, Pathologic * physiopathology MeSH
- Proto-Oncogene Protein c-ets-1 MeSH
- Proto-Oncogene Proteins c-ets MeSH
- Proto-Oncogene Proteins genetics metabolism MeSH
- Proto-Oncogenes physiology MeSH
- Transcription Factors genetics metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Names of Substances
- Proto-Oncogene Protein c-ets-1 MeSH
- Proto-Oncogene Proteins c-ets MeSH
- Proto-Oncogene Proteins MeSH
- Transcription Factors MeSH
