Chemistry / Kimya

Permanent URI for this collectionhttps://hdl.handle.net/11147/4072

Browse

Filters

2016 - 2019122020 - 202415

Settings

Department: search.filters.department.İzmir Institute of Technology. Bioengineering

Search Results

Now showing 1 - 10 of 27
  • Article
    Citation - Scopus: 3
    Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform
    (Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
    Plasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots
    (Wiley, 2024) Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit Hakan
    This study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.image
  • Article
    Citation - WoS: 17
    Citation - Scopus: 15
    Antiproliferative and Apoptotic Effects of Olive Leaf Extract Microcapsules on Mcf-7 and A549 Cancer Cells
    (American Chemical Society, 2023) Bal, Yıldız; Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
    Alginate microcapsules are a talented means for the delivery of broad curative biomacromolecules. In this study, we immobilized olive leaf extract (OLE) by calcium alginate (CA) and chitosan-coated CA (CCA) and characterized the OLE-loaded CA and CCA. The cytotoxic effect, the cell cycle arrest, and the apoptotic effect of OLE and its microcapsules were investigated against breast adenocarcinoma (MCF-7) and lung carcinoma (A549). As a result, the loading capacity of OLE-CA and OLE-CCA was found to be 80 and 99%, respectively, in optimal conditions. Also, OLE-CA and OLE-CCA were characterized by unique FTIR peaks and morphological display relative to the empty CCA microcapsules. The cytotoxicity analysis showed that the IC50 values of OLE-CA and OLE-CCA were determined to be 312 and 0.94 μg mL-1 against A549, respectively, whereas these were found to be 865.4 and 425.5 μg mL-1 for MCF-7 cells. On the other hand, the OLE microcapsules did not possess in any concentration of cytotoxic influence on the BEAS 2B healthy cell line. Also, the exposure of OLE-CCA to MCF-7 and A549 resulted in the arrest of more MCF-7 and A549 cells at the G0/G1 phase compared to the OLE. A549 and MCF-7 cells were predominantly found in the late apoptosis phase and necrosis phase, respectively. Optical microscopy images confirmed that OLE microcapsules were more effective against MCF-7 and A549 than free OLE. The present work suggested that the OLE microcapsules might be administered as nutrition supplements for cancer therapy. © 2023 The Authors. Published by American Chemical Society.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 6
    Immobilization of Olive Leaf Extract With Chitosan Nanoparticles as an Adjunct To Enhance Cytotoxicity
    (American Chemical Society, 2023) Özdamar, Burcu; Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
    We immobilized the olive leaf extract (OLE) with chitosannanoparticles(CNPs) by optimizing the effect of various immobilization conditions,and OLE-loaded CNPs (OLE-CNPs) were then elaborately characterizedphysicochemically by scanning electron microscopy (SEM), Fourier transforminfrared (FT-IR) spectroscopy, dynamic light scattering (DLS), andatomic force microscopy (AFM). Under optimal conditions, CNPs wereable to accommodate the OLE with a loading capacity of 97.5%. Theresulting OLE-CNPs had a spherical morphology, and their average diameterwas approximately 100 nm. The cytotoxic influence, cell cycle distribution,and apoptosis stage of OLE and OLE-CNPs were analyzed on lung carcinoma(A549) and breast adenocarcinoma (MCF-7) cell lines. In an in vitrocytotoxic assay, IC50 values of OLE-CNPs were determinedto be 540 & mu;g/mL for A549 and 810 & mu;g/mL for MCF-7. Thetreatment of both A549 and MCF-7 with OLE-CNPs caused the highestcell arrest in G0/G1 in a dose-independent manner. OLE-CNPs affectedcell cycle distribution in a manner different from free OLE treatmentin both cancer cells. A549 and MCF-7 cells were predominantly foundin the late apoptosis and necrosis phases, respectively, upon treatmentof 1000 & mu;M OLE-CNPs. Our results suggest that CNPs enhance theutility of OLEs as nutraceuticals in cancer and that OLE-CNPs canbe utilized as an adjunct to cancer therapy.
  • Book Part
    Citation - Scopus: 3
    Tissue Engineering Applications of Marine-Based Materials
    (Springer, 2022) Polat, Hürriyet; Zeybek, Nuket; Polat, Mehmet
    Tissue engineering is a promising approach in replacing or improving tissues lost or has become nonviable due to disease or trauma by the use of scaffold materials by combining engineering and biochemical/physicochemical methods. Its purpose is to create suitable matrices that support cell differentiation and proliferation toward the formation of new and functional tissue. Marine-based natural compounds are potential scaffold feedstock material in tissue engineering owing to their biocompatibility and biodegradability while providing excellent biochemical/physicochemical properties. Numerous application areas and various fabrication routes techniques described in the literature attest to the importance of these materials in tissue regeneration. This review has been carried to merge the information from a large number of studies on the marine-based scaffold materials in tissue engineering into a coherent summary. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.
  • Article
    Citation - WoS: 9
    Citation - Scopus: 8
    Astragalus Saponins, Astragaloside Vii and Newly Synthesized Derivatives, Induce Dendritic Cell Maturation and T Cell Activation
    (MDPI, 2023) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, Duygu
    Astragaloside VII (AST VII), a triterpenic saponin isolated from Astragalus species, shows promise as a vaccine adjuvant, as it supported a balanced Th1/Th2 immune response in previous in vivo studies. However, the underlying mechanisms of its adjuvant activity have not been defined. Here, we investigated the impact of AST VII and its newly synthesized semi-synthetic analogs on human whole blood cells, as well as on mouse bone marrow-derived dendritic cells (BMDCs). Cells were stimulated with AST VII and its derivatives in the presence or absence of LPS or PMA/ionomycin and the secretion of cytokines and the expression of activation markers were analyzed using ELISA and flow cytometry, respectively. AST VII and its analogs increased the production of IL-1β in PMA/ionomycin-stimulated human whole blood cells. In LPS-treated mouse BMDCs, AST VII increased the production of IL-1β and IL-12, and the expression of MHC II, CD86, and CD80. In mixed leukocyte reaction, AST VII and derivatives increased the expression of the activation marker CD44 on mouse CD4+ and CD8+ T cells. In conclusion, AST VII and its derivatives strengthen pro-inflammatory responses and support dendritic cell maturation and T cell activation in vitro. Our results provide insights into the mechanisms of the adjuvant activities of AST VII and its analogs, which will be instrumental to improve their utility as a vaccine adjuvant. © 2023 by the authors.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability
    (Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
    Alpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.
  • Conference Object
    Citation - WoS: 1
    Immunomodulatory Mechanisms of Astragalus Saponins
    (Wiley, 2021) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, Duygu
  • Article
    Citation - WoS: 16
    Citation - Scopus: 18
    A Novel Thermostable Xylanase From Geobacillus Vulcani Gs90: Production, Biochemical Characterization, and Its Comparative Application in Fruit Juice Enrichment
    (Wiley, 2021) Algan, Müge; Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
    Xylanases have great attention to act as a potential role in agro-industrial processes. In this study, production, characterization, and fruit juice application of novel xylanase from thermophilic Geobacillus vulcani GS90 (GvXyl) were performed. GvXyl was purified via acetone precipitation and gel-filtration chromatography. The results showed that GvXyl had 1,671.4 U/mg of specific activity and optimally worked at pH 8 and 55 degrees C. It was also active in a wide pH (3-9) and temperature (30-90oC) ranges. GvXyl was highly stable at 90oC and relatively stable at pH 3-9. The kinetic parameters of GvXyl were obtained as K-m, V-max, and k(cat); 10.2 mg/ml, 4,104 mu mol min(-1) mg(-1), and 3,542.6 s(-1), respectively. GvXyl had higher action than commercial xylanase in fruit juice enrichment. These results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability. Practical applications Polysaccharides include starch, pectin, and hemicellulose create problems by lowering fruit juice quality in beverages. To overcome this problem, various clarification processes might be applied to natural fruit juices. Even though chemicals are widely used for this purpose, recently enzymes including xylanases are preferred for obtaining high-quality products. In this study, we reported the production and biochemical characterization of novel thermostable xylanase from thermophilic G. vulcani GS90 (GvXyl). Also, apple and orange juice enrichment were performed with the novel xylanase to increase the quality in terms of yield, clarity, and reducing sugar substance. The improved quality features of apple and orange juices with GvXyl was then compared to commercially available beta-1,4-xylanase. The results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability.
  • Article
    Citation - WoS: 43
    Citation - Scopus: 46
    Glucuronoxylan-Based Quince Seed Hydrogel: a Promising Scaffold for Tissue Engineering Applications
    (Elsevier, 2021) Güzelgülgen, Meltem; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
    Natural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuron-oxylanbased quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH and crosslinker glutaraldehyde (GTA) concentrations. Structural characterization of QSH was done by Fourier Transform Infrared Spectroscopy (MR). Furthermore, morphological and mechanical investigation of QSH was performed by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The protein adsorption test revealed the suitability of QSH for cell attachment. Biocompatibility of QSH was confirmed by culturing NIH-3T3 mouse fibroblast cells on it. Cell viability and proliferation results revealed that optimum parameters for cell viability were 2 mg mi(-1)of QSH and 0.03 M GTA. SEM and DAPI staining results indicated the formation of spheroids with a diameter of approximately 300 pm. Furthermore, formation of extracellular matrix (ECM) microenvironment was confirmed with the Collagen Type-I staining. Here, it was demonstrated that the fabricated QSH is a promising scaffold for 3D cell culture and tissue engineering applications provided by its highly porous structure, remarkable swelling capacity and high biocompatibility. (C) 2021 Published by Elsevier B.V.