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Extracellula r matri x (ECM)-derived hydrogels are in demand for use in lung tissue engineering to mimic the native microenvironment of cells in vitro. Decellularization of native tissues has been pursued for preser v i n g organotypic ECM while eliminating cellular content and reconstitution into scaffolds which allows re-cellularization for modeling homeostasis, regeneration, or diseases. Achieving mechanical stabi l i t y and understanding the effects of the decellularization process on mechanical parameters of the reconstituted ECM hydrogels present a challenge in the field. Stiffness and viscoelasticity are important characteristics of tissue mechanics that regulate crucial cellular processes and their in vitro representation in engineered models is a current aspiration. The effect of decellulariza-tion on viscoelastic properties of resulting ECM hydrogels has not yet been addressed. The aim of this study was to establish bovine lung tissue decellularization for the first time via pursuing four different protocols and characterization of reconstituted decellularized lung ECM hydrogels for biochemical and mechanical properties. Our data reveal that bovine lungs provide a reproducible alternative to human lungs for disease modeling with optimal retention of ECM components upon decellularization. We demonstrate that the decellularization method significa n t l y affects ECM content, stiffness, and viscoelastic properties of resulting hydrogels. Lastly, we examined the impact of these aspects on viabi l i t y , morphology, and growth of lung cancer cells, healthy bronchial epithelial cells, and patient-derived lung organoids., This work was funded by the International Fellowship for Outstanding Researchers Program of Scientific and Technological Research Council of Turkey (TÜBİTAK) (grant no. 118C238) and Marie Sklodowska-Curie Individual Fellowship (MiTuMi, grant no. 101032602).

One of the key challenges in engineering three-dimensional tissue constructs is the development of a mature microvascular network capable of supplying sufficient oxygen and nutrients to the tissue. Recent angiogenic therapeutic strategies have focused on vascularization of the constructed tissue, and its integration in vitro; these strategies typically combine regenerative cells, growth factors (GFs) with custom-designed biomaterials. However, the field needs to progress in the clinical translation of tissue engineering strategies. The article first presents a detailed description of the steps in neovascularization and the roles of extracellular matrix elements such as GFs in angiogenesis. It then delves into decellularization, cell, and GF-based strategies employed thus far for therapeutic angiogenesis, with a particularly detailed examination of different methods by which GFs are delivered in biomaterial scaffolds. Finally, interdisciplinary approaches involving advancement in biomaterials science and current state of technological development in fabrication techniques are critically evaluated, and a list of remaining challenges is presented that need to be solved for successful translation to the clinics., Scientific and Technological Research Council of Turkey (TÜBİTAK); ARDEB 1001 Scientific and Technological Research Projects Funding Program; 3501 National Young Researchers Career Development Program; Koç University Seed Fund

During the last couple of decades considerable research efforts have been directed towards the synthesis and coating of iron oxide nanoparticles (IONPs) for biomedical applications. To address the current limitations, recent studies have focused on the design of new generation nanoparticle systems whose internalization and targeting capabilities have been improved through surface modifications. This review covers the most recent challenges and advances in the development of IONPs with enhanced quality, and biocompatibility for various applications in biotechnology and medicine., NA

Two bisphosphonic acid-functionalized cross-linkers (one novel) with different spacer chain characteristics were synthesized and incorporated into hydrogels by copolymerization with 2-hydroxyethyl methacrylate at different ratios to control the hydrogels' swelling, mechanical properties, and ability to support mineralization for biomedical applications. The cross-linkers were synthesized by reaction of 2-isocyanatoethyl methacrylate and bisphosphonated diamines followed by selective dealkylation of the bisphosphonate ester groups. The hydrogels provide in vitro growth of carbonated apatite, morphology affected by the cross-linker structure. The hydrogels exhibit a high Young's modulus E (up to 400 kPa) and can sustain up to 10.2 +/- 0.1 MPa compressive stresses. E and hence the cross-link density significantly increases upon mineralization reflecting the formation of many bisphosphonate BP-Ca2+ bonds acting as additional cross-links. Cyclic mechanical tests reveal self-recoverability of hydrogels because of reversible nature of BP-Ca2+ bonds. The results suggest that these cross-linkers can add calcium-binding abilities to hydrogels synthesized from any monomer and improve their mechanical, swelling, and mineralization properties and hence are potentially useful materials for biomedical applications., Boğaziçi University Research Fund; Turkish Academy of Sciences (TÜBA)

This study reports the potential of a unique functional composite for anti-icing applications. To date, various ionic salt formulations have been applied to prevent ice accumulation on surfaces. However, salt can be removed by external factors and large amounts must be used to attain anti-icing properties. Incorporating hydrophilic salts into hydrophobic mediums and controlled release of specific agents can provide effective solution to reduce ice accumulation on surfaces. Here, we developed functional polymer composites with salt pockets of altered ionic salts consisting of potassium formate (KCOOH), sodium chloride (NaCl), or magnesium chloride (MgCl2). We dissolved ionic salts in hydrophilic gel domains and dispersed in a hydrophobic styrene-butadiene-styrene polymer matrix. Na+ and Cl- ions delayed ice formation by 42.6 min at -2 degrees C compared to that for unmodified surfaces. Functional composites prepared with the NaCl ionic salt exhibited better anti-icing behavior at -2 degrees C because of their high concentration compared to that of the composites prepared with KCOOH and MgCl2 ionic salts. We also characterized the release of ionic salts from composite-modified hydrophobic medium separately up to 118 days. Furthermore, we monitored freezing of water on composite-incorporated or composite-coated hydrophobic surfaces in a camera-integrated cold chamber with a uniform temperature (-2 degrees C). The results demonstrated significant increases in the delay of freezing on composite-incorporated or composite-coated surfaces compared to that on controls. We observed altered effects of each ionic salt on the mechanical, morphological, and functional properties of the composite-incorporated or composite-coated hydrophobic surfaces. Our results suggested that the efficiency of a polymer composite to promote anti-icing behavior on a surface is directly related to the type and concentration of the particular ionic salt incorporation into the composite. This approach is promising and demonstrates significant potential of the ionic salt embedded within polymer composite-modified hydrophobic surfaces to attain delayed icing function., GENERALI; Turkish Petroleum Refineries Corporation (TUPRAS)

Experimentation of nanomedicine is labor-intensive, time-consuming, and requires costly laboratory consumables. Constructing a reliable mathematical model for such systems is also challenging due to the difficulties in gathering a sufficient number of data points. Artificial neural networks (ANNs) are indicated as an efficient approach in nanomedicine to investigate the cause-effect relationships and predict output variables. Herein, an ANN is adapted into plasmid DNA (pDNA) encapsulated and PEGylated chitosan nanoparticles cross-linked with sodium tripolyphosphate (TPP) to investigate the effects of critical parameters on the transfection efficiencies of nanoparticles. The ANN model is developed based on experimental results with three independent input variables: 1) polyethylene glycol (PEG) molecular weight, 2) PEG concentration, and 3) nanoparticle concentration, along with one output variable as a percentage of green fluorescent protein (GFP) expression, which refers to transfection efficiency. The constructed model is further validated with the leave-p-out cross-validation method. The results indicate that the developed model has good prediction capability and is influential in capturing the transfection efficiencies of different nanoparticle groups. Overall, this study reveals that the ANN could be an efficient tool for nanoparticle-mediated gene delivery systems to investigate the impacts of critical parameters in detail with reduced experimental effort and cost., Advanced NanoBiomed Research, 2 (1), ISSN:2699-9307

Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barrier for clinical translation of these materials. Here, we report the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels leads to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two-fold with anthracene conjugation during photopolymerization and photodimerization. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision., Scientific and Technological Research Council of Turkey (TÜBİTAK), International Support Program (COST Action - European Cooperation in Science and Technology); Koç University Seed Fund; Presidency of Turkey, Presidency of Strategy and Budget.

Biohybrid microswimmers exploit the swimming and navigation of a motile microorganism to target and deliver cargo molecules in a wide range of biomedical applications. Medical biohybrid microswimmers suffer from low manufacturing yields, which would significantly limit their potential applications. In the present study, a biohybrid design strategy is reported, where a thin and soft uniform coating layer is noncovalently assembled around a motile microorganism.Chlamydomonas reinhardtii(a single-cell green alga) is used in the design as a biological model microorganism along with polymer-nanoparticle matrix as the synthetic component, reaching a manufacturing efficiency of approximate to 90%. Natural biopolymer chitosan is used as a binder to efficiently coat the cell wall of the microalgae with nanoparticles. The soft surface coating does not impair the viability and phototactic ability of the microalgae, and allows further engineering to accommodate biomedical cargo molecules. Furthermore, by conjugating the nanoparticles embedded in the thin coating with chemotherapeutic doxorubicin by a photocleavable linker, on-demand delivery of drugs to tumor cells is reported as a proof-of-concept biomedical demonstration. The high-throughput strategy can pave the way for the next-generation generation microrobotic swarms for future medical active cargo delivery tasks., Koç University Seed Fund; Max Planck Society; Koç University Visiting Scholar Program

An ultrafast and convenient method for PEGylation of chitosan nanoparticles has been established through a photopolymerization reaction between the acrylate groups of PEG and methacrylated-chitosan nanoparticles. The nanoparticle characteristics under physiological pH conditions were optimized through altered PEG chain length, concentration and duration of UV exposure. The method developed here has potential for clinical translation of chitosan nanoparticles. It also allows for the scalable and fast synthesis of nanoparticles with colloidal stability., Scientific and Technological Research Council of Turkey (TÜBİTAK); European Union (European Union); Horizon 2020; European Union COST Action; Presidency of Turkey; Presidency of Strategy and Budget

Type 1 diabetes (T1D) is an autoimmune disease characterized by destruction of pancreatic β cells. One of the promising therapeutic approaches in T1D is the transplantation of islets; however, it has serious limitations. To address these limitations, immunotherapeutic strategies have focused on restoring immunologic tolerance, preventing transplanted cell destruction by patients’ own immune system. Macrophage-derived chemokines such as chemokine-ligand-22 (CCL22) can be utilized for regulatory T cell (Treg) recruitment and graft tolerance. Stellate cells (SCs) have various immunomodulatory functions: recruitment of Tregs and induction of T-cell apoptosis. Here, we designed a unique immune-privileged microenvironment around implantable islets through overexpression of CCL22 proteins by SCs. We prepared pseudoislets with insulin-secreting mouse insulinoma-6 (MIN6) cells and human SCs as a model to mimic naive islet morphology. Our results demonstrated that transduced SCs can secrete CCL22 and recruit Tregs toward ​the implantation site in vivo. This study is promising to provide a fundamental understanding of SC-islet interaction and ligand synthesis and transport from SCs at the graft site for ensuring local immune tolerance. Our results also establish a new paradigm for creating tolerable grafts for other chronic diseases such as diabetes, anemia, and central nervous system (CNS) diseases, and advance the science of graft tolerance., Scientific and Technological Research Council of Turkey (TÜBİTAK)

We report here a method for the synthesis of a unique hybrid gel system for the sustained delivery of P2X7 receptor (P2X7R) antagonist. P2X7R has been reported as a key mediator in inflammatory processes and controlled delivery of this molecule would be critical for the treatment of inflammatory arthritis. The hybrid gel designed here for the sustained delivery of P2X7R antagonists is based on crosslinked hydrophobic styrene-butadiene-styrene (SBS) polymer as a continuous network, where hydrogel particles prepared with hydrophilic poly(ethylene glycol) (PEG) were embedded into this system. PEG hydrogel particle-incorporated SBS gels were characterized through electron microscopy, water contact angle observations, and strong mechanical properties were confirmed through nanoindentation measurements. The release of P2X7R antagonist from these hybrid hydrogel-elastomer system demonstrated a sustained drug release profile up to 28 days at physiological pH, which was not observed in earlier reports. We obtained drug release percentages ranging from 49.72% to 93.04% which indicated the tunability of release through SBS crosslinking and hydrophilic/hydrophobic nature of SBS. This tunability is significant to achieve simultaneous improvements in drug efficacy with reduced side effects. CellTiter-Glo luminescence measurements using human kidney cells revealed that these networks are non-toxic and highly biocompatible with percent cell viabilities of higher than 85%. The approach presented here with crosslinked, amphiphilic and elastic SBS gel systems is not only promising for extended release of P2X7R antagonist but could also allow for incorporation of different molecules so that simultaneous/sequential and extended release profiles for therapeutic molecules could be achieved., GENERALI; Koç University Seed Fund Program

The objective of this study was to develop thin, biocompatible, and biofunctional hydrogel-coated small-sized nanoparticles that exhibit favorable stability, viability, and specific cellular uptake. This article reports the coating of magnetic iron oxide nanoparticles (MIONPs) with covalently cross-linked biofunctional polyethylene glycol (PEG) hydrogel. Silanized MIONPs were derivatized with eosin Y, and the covalently cross-linked biofunctional PEG hydrogel coating was achieved via surface-initiated photopolymerization of PEG diacrylate in aqueous solution. The thickness of the PEG hydrogel coating, between 23 and 126 nm, was tuned with laser exposure time. PEG hydrogel-coated MIONPs were further functionalized with the fibronectin-derived arginine-glycine-aspartic acid-serine (RGDS) sequence, in order to achieve a biofunctional PEG hydrogel layer around the nanoparticles. RGDS-bound PEG hydrogel-coated MIONPs showed a 17-fold higher uptake by the human cervical cancer HeLa cell line than that of amine-coated MIONPs. This novel method allows for the coating of MIONPs with nano-thin biofunctional hydrogel layers that may prevent undesirable cell and protein adhesion and may allow for cellular uptake in target tissues in a specific manner. These findings indicate that the further biofunctional PEG hydrogel coating of MIONPs is a promising platform for enhanced specific cell targeting in biomedical imaging and cancer therapy., College of Engineering at Koc University; Marie Curie International Reintegration Grant

Background: Insulin-degrading enzyme (IDE) is an allosteric Zn+2 metalloprotease involved in the degradation of many peptides including amyloid-beta, and insulin that play key roles in Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM), respectively. Therefore, the use of therapeutic agents that regulate the activity of IDE would be a viable approach towards generating pharmaceutical treatments for these diseases. Crystal structure of IDE revealed that N-terminal has an exosite which is similar to 30 angstrom away from the catalytic region and serves as a regulation site by orientation of the substrates of IDE to the catalytic site. It is possible to find small molecules that bind to the exosite of IDE and enhance its proteolytic activity towards different substrates.Methodology/Principal Findings: In this study, we applied structure based drug design method combined with experimental methods to discover four novel molecules that enhance the activity of human IDE. The novel compounds, designated as D3, D4, D6, and D10 enhanced IDE mediated proteolysis of substrate V, insulin and amyloid-b, while enhanced degradation profiles were obtained towards substrate V and insulin in the presence of D10 only. Conclusion/Significance: This paper describes the first examples of a computer-aided discovery of IDE regulators, showing that in vitro and in vivo activation of this important enzyme with small molecules is possible., NA

The cyclobutane pyrimidine dimer (CPD) and 6-4 lesion formations along with the specific breaks on strands are the most common type of DNA damage caused by Ultraviolet light (UV) irradiation. CPD photolyase I and II construct two subfamilies of flavoproteins, which have recognition and repair capabilities of CPD sites on both single stranded (ssDNA) and double stranded DNA (dsDNA) with the aid of blue light energy. The other types of flavoprotein family consist of cryptochromes (CRY) that act as photoreceptors in plants, or circadian rhythm regulators in animals. Recent findings showed that a specific type of Cryptochrome-Drosophila, Arabidopsis, Synechocystis, Human (CRY-DASH) has photorepair activity on ssDNA. In this work, real-time interactions between CRY-DASH and ss/dsDNA as well as the interactions between Vibrio cholerae photolyase (VcPHR) and ss/dsDNA were investigated using Surface Plasmon Resonance (SPR). The interactions were then characterized and compared in order to investigate the effect of different types of flavoprotein on UV damaged ss/dsDNA. SPR results confirm the specific binding of VcPHR and CRY-DASH with UV treated DNA. This study is the first instance to quantify the interactions of UV treated and untreated DNA with flavoproteins., College of Engineering at Koc University in Turkey; Scientific and Technological Research Council of Turkey (TÜBİTAK); Marie Curie FP7-IRG-DMIOL; Turkish Academy of Sciences (TÜBA)-GEBİP

Polymer composites consisted of small hydrophilic pockets homogeneously dispersed in a hydrophobic polymer matrix are important in many applications where controlled release of the functional agent from the hydrophilic phase is needed. As an example, a release of biomolecules or drugs from therapeutic formulations or release of salt in anti-icing application can be mentioned. Here, we report a method for preparation of such a composite material consisted of small KCOOH salt pockets distributed in the styrene-butadiene-styrene (SBS) polymer matrix and demonstrate its effectiveness in anti-icing coatings. The mixtures of the aqueous KCOOH and SBS-cyclohexane solutions were firstly stabilized by adding silica nanoparticles to the emulsions and, even more, by gelation of the aqueous phase by agarose. The emulsions were observed in optical microscope to check its stability in time and characterized by rheological measurements. The dry composite materials were obtained via casting the emulsions onto the glass substrates and evaporations of the organic solvent. Composite polymer films were characterized by water contact angle (WCA) measurements. The release of KCOOH salt into water and the freezing delay experiments of water droplets on dry composite films demonstrated their anti-icing properties. It has been concluded that hydrophobic and thermoplastic SBS polymer allows incorporation of the hydrophilic pockets/phases through our technique that opens the possibility for controlled delivering of anti-icing agents from the composite., Turkish Petroleum Oil Refineries (TÜPRAŞ) Company