Browsing by Subject "Biomineralization"

Now showing 1 - 12 of 12

Open Access
Bioactive peptide nanofibers for bone tissue regeneration
(2017-06) Tansık, Gülistan
Replacement and repair of bone tissue that is lost due to fractures, tumor resection, degenerative diseases and infections still remain major clinical challenges. Autografting, allografting and xenografting are the current strategies for the treatment of bone defects. However, these strategies cause problems such as immunological response and disease transmission in clinical applications. To overcome these limitations, regeneration of new bone can be induced by the use of synthetic bioactive materials. One of the most promising strategies is to develop synthetic scaffolds mimicking the functional components of the extracellular matrix (ECM). Biomineralization is mineralization carried out by living organisms. Glycosaminoglycans have crucial roles in biomineralization and enhance the functions of growth factors involved in biomineralization. Success in bone regeneration studies requires a thorough understanding of the necessary conditions for triggering biomineralization during the bone tissue formation process. In this study, the effect of bioactive and biocompatible peptide nanofibers on osteogenic differentiation, biomineralization and bone tissue regeneration are investigated under in vitro and in vivo conditions. In the first chapter, bone tissue composition, the clinical need for bone regeneration and general principles in bone tissue engineering are discussed. Bone tissue regeneration strategies are also highlighted in this part, with emphasis on peptide amphiphiles and self-assembly behavior. In the second chapter, a fully synthetic, extracellular matrix-mimetic peptide nanofiber system is described for enhancing the biomineralization and regeneration of bone tissue. This nanostructural environment forms artificial intracellular networks and supports biomineralization by providing cell-material and protein-material interactions. In the third chapter, effect of osteoinductive peptide nanofibers on osteogenic differentiation of rat mesenchymal stem cells (MSCs) were investigated. In the fourth chapter, the natural biomineralization process in bone tissue was mimicked on peptide nanofibers and the effect of this system on the osteogenic differentiation of osteoblast-like cells was investigated. In the fifth chapter, a dentin-mimetic peptide amphiphile (SpDSp-PA) molecule that is capable of emulating the structure and function of dentin phosphoprotein was designed and its capacity to support the deposition of hydroxyapatite and survival and biomineralization of osteoblast-like cells was evaluated.
Open Access
Biomineralization of calcium phosphate crystals controlled by protein-protein interactions
(American Chemical Society, 2019) Duman, Elif; Şahin-Kehribar, Ebru; Ahan, Recep Erdem; Yuca, Esra; Şeker, Urartu Özgür Şafak
Hydroxyapatite (HAP) is the major biomineral of bone. Despite the large number of studies addressing HAP formation, a fundamental understanding of the critical roles of HAP-forming proteins in vitro is needed. Effects of two HAP-interacting proteins, osteocalcin (OCN) and osteopontin (OPN), on HAP formation was investigated via in vitro biomineralization experiments, and their outcomes on the crystal structure of calcium phosphate (CaP) was revealed. Our data suggest that OCN concentration is negatively correlated with crystal formation rate and crystal size, yet the presence of OCN leads to a more ordered HAP crystal formation. On the other hand, OPN protein promotes faster formation of CaP crystals potentially working as a growth site for mineral formation, and it decreases the Ca:P ratio. This effect results in a shift from HAP-type minerals to less ordered crystals. The crystal size, shape, and Ca:P ratio can be tuned to design improved mammalian hard tissue environment-mimicking matrices by taking advantage of the OCN and OPN proteins on crystal formation. We believe our current findings will lead to innovative approaches for bone biomineralization in regenerative medicine.
Open Access
Biomineralization with engineered cellular systems
(2019-08) Ergül, Elif
Hydroxyapatite (HAP) is the final product of bone biomineralization process and HAP formation is controlled by proteins, enzymes and small molecules secreted to extracellular matrix (ECM). Among these molecules, alkaline phosphatase (ALP) leads formation of HAP crystals and noncollagenous proteins control crystal nucleation and growth, and inhibit crystal formation. Osteocalcin (OCN) and osteopontin (OPN), are the most abundant noncollagenous proteins in ECM, which controls mineralization events. In this study, effect of OCN and OPN on HAP crystal formation was studied in order to achieve controlled crystal growth. In vitro biomineralization assays were conducted to understand the effect of OCN and OPN on the crystal structure of as formed minerals. While OCN decreases crystal growth rate and inhibit mineralization, which leads to more uniform crystal formation, OPN provides faster mineral formation with reduced Ca/P ratio. Moreover, a mammalian engineered cell line was constructed to achieve expression of bone extracellular matrix (ECM) proteins. For this purpose, genetic cassettes were produced to express OCN and OPN proteins, which are the most common non-collagen proteins that control bone mineral formation. By this way, production of bone type minerals with controlled size, shape and Ca/P ratio can be possible. Our system provides a truly biomimetic approach to HAP formation compared to chemical synthesis methods in literature. We believe our current findings will lead to innovative approaches for bone biomineralization in regenerative medicine and bone tissue engineering.
Open Access
A comprehensive methodology for determining the most informative mammographic features
(2013) Wu, Y.; Alagoz O.; Ayvaci, M.U.S.; Munoz Del Rio, A.; Vanness, D.J.; Woods, R.; Burnside, E.S.
This study aims to determine the most informative mammographic features for breast cancer diagnosis using mutual information (MI) analysis. Our Health Insurance Portability and Accountability Act-approved database consists of 44,397 consecutive structured mammography reports for 20,375 patients collected from 2005 to 2008. The reports include demographic risk factors (age, family and personal history of breast cancer, and use of hormone therapy) and mammographic features from the Breast Imaging Reporting and Data System lexicon. We calculated MI using Shannon's entropy measure for each feature with respect to the outcome (benign/malignant using a cancer registry match as reference standard). In order to evaluate the validity of the MI rankings of features, we trained and tested naïve Bayes classifiers on the feature with tenfold cross-validation, and measured the predictive ability using area under the ROC curve (AUC). We used a bootstrapping approach to assess the distributional properties of our estimates, and the DeLong method to compare AUC. Based on MI, we found that mass margins and mass shape were the most informative features for breast cancer diagnosis. Calcification morphology, mass density, and calcification distribution provided predictive information for distinguishing benign and malignant breast findings. Breast composition, associated findings, and special cases provided little information in this task. We also found that the rankings of mammographic features with MI and AUC were generally consistent. MI analysis provides a framework to determine the value of different mammographic features in the pursuit of optimal (i.e., accurate and efficient) breast cancer diagnosis. © 2013 Society for Imaging Informatics in Medicine.
Open Access
Dentin phosphoprotein mimetic peptide nanofibers promote biomineralization
(WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim, 2019) Gülseren, Gülcihan; Tansik, Gülistan; Garifullin, Ruslan; Tekinay, Ayse B.; Güler, Mustafa O.
Dentin phosphoprotein (DPP) is a major component of the dentin matrix playing crucial role in hydroxyapatite deposition during bone mineralization, making it a prime candidate for the design of novel materials for bone and tooth regeneration. The bioactivity of DPP‐derived proteins is controlled by the phosphorylation and dephosphorylation of the serine residues. Here an enzyme‐responsive peptide nanofiber system inducing biomineralization is demonstrated. It closely emulates the structural and functional properties of DPP and facilitates apatite‐like mineral deposition. The DPP‐mimetic peptide molecules self‐assemble through dephosphorylation by alkaline phosphatase (ALP), an enzyme participating in tooth and bone matrix mineralization. Nanofiber network formation is also induced through addition of calcium ions. The gelation process following nanofiber formation produces a mineralized extracellular matrix like material, where scaffold properties and phosphate groups promote mineralization. It is demonstrated that the DPP‐mimetic peptide nanofiber networks can be used for apatite‐like mineral deposition for bone regeneration.
Open Access
Design, synthesis and characterization of bioinspired nanomaterials for engineering and biomedicine
(2014) Ceylan, Hakan
Nature is an inspirational school for materials scientists. Natural selection process puts a massive pressure on biological organisms giving rise to effective strategies for fabricating materials, which generally outperform their man-made counterparts. Mimicking physical and chemical features of biological materials can greatly aid in overcoming existing design constraints of engineering and medicine. In this dissertation, a reductionist, bottom-up approach is demonstrated to recapitulate biological functionalities in fully-synthetic hybrid constructs. For material design, the potential of short, rationally-designed peptides for programmed organization into nanostructured materials is explored. The resulting nano-ordered materials exhibit multifunctional and adaptive properties, which can be tailored by the information within monomeric peptide sequences as well as the emerging properties upon their self-assembly. In light of these, design, synthesis and characterization of the prototypes of nanostructured functional materials are described in the context of regenerative medicine and biomineralization.
Open Access
Genetically programmed engineered cells for biomaterials synthesis
(2021-01) Kırpat, Büşra Merve
Several organisms can process nanomaterials and producing in various sizes and morphologies in mild conditions by utilizing specific proteins. In sea sponges, silicatein proteins play a key role in synthesizing silica nanoparticles the precursor silicic acid. Silaffin proteins in diatoms can also biomineralize silica. One subunit of silaffin called R5 peptide has a key role for nucleation and initiation of the nanoparticle formation and it has been shown that bacteria synthesized R5 peptide has ability to precipitate silica structures. These silica nanostructures can be utilized in many areas. Silica-based cements take attentions to make them useful in restorative dentistry and endodontics. In this work, a synthetic cell system has reprogrammed autotransporter (Ag43) system to display R5 peptide fused with fluorescent proteins. After displaying the fused proteins on the surface of bacteria or secreting them into environment, whole cell or the proteins are used to precipitate silica in the presence of precursor such as tetramethyl orthosilicate (TMOS). These silica structures are used to evaluate their in vitro effects on the proliferation of dental pulp stem cells (DPSCs) and their osteogenesis.
Open Access
A glycosaminoglycan mimetic peptide nanofiber gel as an osteoinductive scaffold
(Royal Society of Chemistry, 2016) Tansik, G.; Kilic, E.; Beter, M.; Demiralp, B.; K.Sendur, G.; Can, N.; Ozkan, H.; Ergul, E.; Güler, Mustafa O.; Tekinay, A. B.
Biomineralization of the extracellular matrix (ECM) plays a crucial role in bone formation. Functional and structural biomimetic native bone ECM components can therefore be used to change the fate of stem cells and induce bone regeneration and mineralization. Glycosaminoglycan (GAG) mimetic peptide nanofibers can interact with several growth factors. These nanostructures are capable of enhancing the osteogenic activity and mineral deposition of osteoblastic cells, which is indicative of their potential application in bone tissue regeneration. In this study, we investigated the potential of GAG-mimetic peptide nanofibers to promote the osteogenic differentiation of rat mesenchymal stem cells (rMSCs) in vitro and enhance the bone regeneration and biomineralization process in vivo in a rabbit tibial bone defect model. Alkaline phosphatase (ALP) activity and Alizarin red staining results suggested that osteogenic differentiation is enhanced when rMSCs are cultured on GAG-mimetic peptide nanofibers. Moreover, osteogenic marker genes were shown to be upregulated in the presence of the peptide nanofiber system. Histological and micro-computed tomography (Micro-CT) observations of regenerated bone defects in rabbit tibia bone also suggested that the injection of a GAG-mimetic nanofiber gel supports cortical bone deposition by enhancing the secretion of an inorganic mineral matrix. The volume of the repaired cortical bone was higher in GAG-PA gel injected animals. The overall results indicate that GAG-mimetic peptide nanofibers can be utilized effectively as a new bioactive platform for bone regeneration. © 2016 The Royal Society of Chemistry.
Open Access
A living material platform for the biomineralization of biosilica
(Elsevier B.V., 2022-12-15) Kırpat Konak, Büşra Merve; Bakar, Mehmet Emin; Ahan, Recep Erdem; Özyürek, Emel Uzunoğlu; Dökmeci, Serap; Şafak Şeker, Urartu Özgür
Nature has a vast array of biomineralization mechanisms. The commonly shared mechanism by many living organisms to form hardened tissues is the nucleation of mineral structures via proteins. Living materials, thanks to synthetic biology, are providing many opportunities to program cells for many functionalities. Here we have demonstrated a living material system for biosilicification. Silaffins are utilized to synthesize silicified cell walls by one of the most abundant organism groups called diatoms. The R5 peptide motif of the silaffins is known for its ability to precipitate silica in ambient conditions. Therefore, various studies have been conducted to implement the silicification activity of R5 in different application areas, such as regenerative medicine and tissue engineering. However, laborious protein purification steps are required prior to silica nanoparticle production in recombinant approaches. In this study, we aimed to engineer an alternative bacterial platform to achieve silicification using released and bacteria-intact forms of R5-attached fluorescent proteins (FP). Hence, we displayed R5-FP hybrids on the cell surface of E. coli via antigen 43 (Ag43) autotransporter system and managed to demonstrate heat-controllable release from the surface. We also showed that the bacteria cells displaying R5-FP can be used in silicification reactions. Lastly, considering the stimulating effect of silica on osteogenic differentiation, we treated human dental pulp stem cells (hDPSCs) with the silica aggregates formed via R5-FP hybrids. Earlier calcium crystal deposition around the hDPSCs was observed. We envision that our platform can serve as a faster and more economical alternative for biosilicification applications, including endodontics. © 2022
Open Access
Mineralized peptide nanofiber gels for enhanced osteogenic differentiation
(Wiley, 2018) Eren, E. D.; Tansik, G.; Tekinay, A. B.; Güler, Mustafa O.
Mineral deposition is observed in both bacterial and eukaryotic organisms through a broad range of mechanisms. Both organic and inorganic components play crucial roles in the formation of mineralized tissues, and acidic proteins are particularly important in this context owing to their ability to stimulate nucleation of minerals. Here, we present negatively-charged self-assembling peptide amphiphile molecules as a template to nucleate calcium phosphate mineralization in a bioactive scaffold environment. Acidic peptide molecules were shown to induce formation of hydroxyapatite like calcium phosphate mineralization, which was characterized by scanning electron microscopy, transmission electron microscopy, thermogravimetric analysis, X-ray diffractometry, oscillatory rheology and atomic force microscopy. The osteoblast-like cells were found to reveal enhanced osteogenic differentiation on pre-mineralized peptide nanofiber networks, suggesting that mineral deposition can be used as a means of enhancing the bioactivity of peptide-based scaffold systems.
Open Access
One-dimensional peptide nanostructure templated growth of iron phosphate nanostructures for lithium-ion battery cathodes
(American Chemical Society, 2016-06) Susapto, H. H.; Kudu, O. U.; Garifullin, R.; Yllmaz, E.; Güler, Mustafa O.
Template-directed synthesis of nanomaterials can provide benefits such as small crystalline size, high surface area, large surface-to-volume ratio, and structural stability. These properties are important for shorter distance in ion/electron movement and better electrode surface/electrolyte contact for energy storage applications. Here nanostructured FePO4 cathode materials were synthesized by using peptide nanostructures as a template inspired by biomineralization process. The amorphous, high surface area FePO4 nanostructures were utilized as a cathode for lithium-ion batteries. Discharge capacity of 155 mAh/g was achieved at C/20 current rate. The superior properties of biotemplated and nanostructured amorphous FePO4 are shown compared to template-free crystalline FePO4.
Open Access
Self-assembled template-directed synthesis of one-dimensional silica and titania nanostructures
(2011) Acar H.; Garifullin, R.; Güler, Mustafa O.
Mineralized biological materials such as shells, skeleton, and teeth experience biomineralization. Biomimetic materials exploit the biomineralization process to form functional organic-inorganic hybrid nanostructures. In this work, we mimicked the biomineralization process by the de novo design of an amyloid-like peptide that self-assembles into nanofibers. Chemically active groups enhancing the affinity for metal ions were used to accumulate silicon and titanium precursors on the organic template. The self-assembly process and template effect were characterized by CD, FT-IR, UV-vis, fluorescence, rheology, TGA, SEM, and TEM. The self-assembled organic nanostructures were exploited as a template to form high-aspect-ratio 1-D silica and titania nanostructures by the addition of appropriate precursors. Herein, a new bottom-up approach was demonstrated to form silica and titania nanostructures that can yield wide opportunities to produce high-aspect-ratio inorganic nanostructures with high surface areas. The materials developed in this work have vast potential in the fields of catalysis and electronic materials. © 2011 American Chemical Society.