Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Blank Frame and Intensity Variation Distortion Detection and Restoration Pipeline for Phase-Contrast Microscopy Time-Lapse Images(Aves, 2024) Ucar, Mahmut; Iheme, Leonardo O.; Onal, Sevgi; Pesen-Okvur, Devrim; Yalcin-Ozuysal, Ozden; Toreyin, Behcet U.; Unay, DevrimIn this study, we propose a preprocessing pipeline for the detection and correction of distorted frames in time-lapse images obtained from phase-contrast microscopy. The proposed pipeline employs the average intensities of frames as a foundational element for the analysis. In order to evaluate the degree of correction required for intensity variance, a normalization technique is applied to the difference between the average intensity of a specific frame and the median average intensity of all frames within the study. Our restoration method increases the histogram similarity between the distorted and non-distorted frames, preserves trans-passing pixels in regions of interest, and mitigates the development of additional distortions. The efficacy of the proposed method was evaluated using 15 395 time-lapse image frames from 27 experiments using our own dataset and 830 time-lapse images from four different experiments obtained from the cell tracking challenge. The results of the validation demonstrate a high degree of numerical and visual accuracy of the proposed pipeline.Article Citation - WoS: 7Citation - Scopus: 8Ascorbic Acid Enhances the Metabolic Activity, Growth and Collagen Production of Human Dermal Fibroblasts Growing in Three-Dimensional (3D) Culture(Gazi Üniversitesi, 2023) Dikici, SerkanTissue engineering (TE) enables the development of functional synthetic substitutes to be replaced with damaged tissues and organs instead of the use of auto or allografts. A wide range of biomaterials is currently in use as TE scaffolds. Among these materials, naturally sourced ones are favorable due to being highly biocompatible and supporting cell growth and function, whereas synthetic ones are advantageous because of the high tunability on mechanical and physical properties as well as being easy to process. Alongside the advantages of synthetic polymers, they mostly show hydrophobic behavior that limits biomaterial-cell interaction and, consequently, the functioning of the developed TE constructs. In this study, we assessed the impact of L-Ascorbic acid 2-phosphate (AA2P) on improving the culture conditions of human dermal fibroblasts (HDFs) growing on a three-dimensional (3D) scaffold made of polycaprolactone (PCL) using emulsion templating. Our results demonstrated that AA2P enhances the metabolic activity and growth of HDFs as well as collagen deposition by them when supplemented in their growth medium at 50 µg/mL concentration. It showed a great potential to be used as a growth medium supplement to circumvent the disadvantages of culturing human cells on a synthetic biomaterial that is not favored in default. AA2P's potential to improve cell growth and collagen deposition may prove an effective way to culture human cells on 3D PCL PolyHIPE scaffolds for various TE applications.Article Modelling Genotoxic Effects of Metal Oxide Nanoparticles Using Qsar Approach(2022) Öksel Karakuş, CeydaWe investigated the application of structure-activity relationship approaches to underpin structural properties that potentially control the genotoxic potential of 9 different metal oxide nanoparticles (CuO, ZnO, NiO, SiO2, TiO2, CeO2, Fe2O3, Fe3O4 and Co3O4). In particular, we compiled a pool of quantum-mechanical, experimental and periodic table-driven descriptors and explored their distinctive contribution to the measured activity (genotoxicity). We first employed a clustered heatmap and parallel coordinates plot for visual exploration of the clusters and outliers of the data and finding corresponding responsible physicochemical descriptors. We then investigated the strength (and direction) of the relationship among descriptors and between descriptors and genotoxicity using similarity metrics. By using orthogonal projections to latent structures (OPLS), we were able to quantify the relative contribution of each descriptor to the genotoxicity of metal oxide nanoparticles. Our results suggested that zeta potential, the ratio of core electrons to valence electrons, Fermi energy and electronegativity were significant predictors of genotoxicity. Such computer-assisted approaches hold considerable promise for maximizing the use of accumulated data in nanotoxicology, prioritizing nanoparticles for further testing and filling data gaps required for hazard assessment processes.Article Citation - WoS: 1Citation - Scopus: 1Expression Profile of Prostaglandin Enzymes in Cystic Endometrial Hyperplasia in Dogs: the Results of a Hypothesis in Clinical Trial(Kafkas Üniversitesi, 2023) Korlu, Yeşim; Yavaş, Özkan; Aktar, Ahmet; Bozkurt, Berkay; Özyiğit, Musa Özgür; Özalp, Gözde RabiaThe expressions of prostaglandin synthesis enzymes and estrogen, progesterone receptors in canine cystic endometrial hyperplasia (CEH) were reported in this manuscript. Uterine tissue samples were collected from bitches with CEH (n=5), CEH-P (Cystic endometrial hyperplasia-Pyometra) (n=5) and healthy-negative control group, CG (n=5). Immunohistochemistry was carried out for the estrogen (ER) and progesterone receptor (PR) detection. Shock-frozen samples were utilized in mRNA extraction and Real-Time PCR was performed. Gene expression of PTGS2/COX2, PTGES, PTGER4, PGFS, PTGFR and PGR were detected higher in the CEH group compared with CG. The PGFS and PTGFR (FP) mRNA expressions were significantly increased in CEH compared with other groups. Expression of progesterone receptor mRNA (PGR) was highest in CEH and statistically different from the CEH-P group (P<0.05). No PR immunostaining was observed. ER staining had been detected in endometrial glands, endometrial stoma and myometrium, however hyperplasic glands in propria mucosa had lower or no ER scores. Based on the results of this study, the high levels of prostaglandin enzymes and low ER scores in CEH could be a preliminary step for the next stages of severe differentiation of endometrium.Research Project Halkalı Neodmiyum Mıknatısla Hücresel Manyetik Levitasyon Tekniği Geliştirilmesi ve Uygulaması(2020) Özçivici, EnginManyetik levitasyon hücresel ve doku düzeyinde biyomühendislik uygulamalarında hücrelerin uzaktan manipülasyonu için önemli bir teknolojidir. Mevcut diamanyetik levitasyon tasarımlarının çogu, sistemin çalısma hacmini ve uygulanabilirligini sınırlayan aynı kutupları birbirine dönük iki blok mıknatıs arasında bir levitasyon haznesi içermektedir. Bu projede, biyofabrikasyon uygulamalarında kullanılmak üzere bu fiziksel sınırlamaları ortadan kaldırmak için halkalı mıknatıs tabanlı bir manyetik levitasyon sistemi olusturulmustur. Projede tanımlanan bu konfigürasyon, levitasyon sırasında besi ortamı veya hücrelerin sisteme transfer edilebilmesini ve sistemden uzaklastırılabilmesini, yüksekliginden bagımsız olarak kültür haznesi kullanılabilmesini ve böylelikle büyük boyutlu canlı yapıların üretilebilmesini ve kültürün sürdürülebilmesini mümkün kılmıstır. Biyofabrikasyon çalısmalarından önce, sistemin canlı hücrelerin levitasyonu için özkütleleri açısından uygunlugu polimerik parçacıklar ile gösterilmistir. Sistemin manyetik odaklama fonksiyonu ve hücrelerin kendi kendine bir araya gelme özelliginden yararlanarak düzenekte milimetre boyutunda 3 boyutlu canlı yapılar olusturulmus ve kültürleri cihaz içerisinde sürdürülmüstür. Burada uygulamaya sunulan manyetik levitasyon cihazı, açık bir operasyon alanı saglaması sebebiyle kültüre levitasyon esnasında ve kolay müdahale olanagı sunmustur. Proje kapsamında besi ortamındaki paramanyetik iyon konsantrasyonunu degistirerek farklı özkütlelere sahip hücre tiplerinin (kök hücre, adiposit ve kanser hücresi) levitasyonu ve 3 boyutlu yapı olusumu için manyetik levitasyon protokolleri olusturulmustur. Hücrelerin levitasyonu için gereken paramanyetik iyon konsantrasyonunun ise besi ortamın özkütlesinin arttırılması ile azaltılabilecegi gösterilmistir. Hücre saglıgı açısından zararsız oldugu proje çalısmasında gösterilmis olan bu teknik, ayrı ayrı olusturulmus 3 boyutlu canlı birimlerinin daha karmasık yapılar üretmek üzere birlesmesine de olanak saglamıstır. Ayrıca proje çıktılarında, halkalı mıknatıs tabanlı levitasyon sisteminin hücrelerden çalısılabilir mRNA izolasyonu saglayabildigi ve gen ifadesi düzeyinde çalısmalar için uygun oldugu gösterilmistir. Sonuç olarak, projede olusturulan manyetik levitasyon sistemi doku mühendisligi, ilaç testi ve kanser arastırmaları gibi çok çesitli uygulamalarda kullanım alanı bulabilecektir.Article Novel Coronavirus Disease: Overview and Recent Situation(İstanbul Üniversitesi-Cerrahpaşa Sağlık Bilimleri Fakültesi, 2020) Öksel, Ceyda; Bilgi, Eyüp; Başlar, Muhammet Semih; Çeşmeli, Selin; Tomak, Aysel; Hanoğlu, Berçem DilanIn the last days of 2019, local hospitals in Wuhan city (population of 11 million) reported several pneumonia cases with unknown etiology among people linked to the Huanan Seafood Wholesale Market. The virus, which is thought to be the source of the unknown viral infection, was first identified as a new type of coronavirus on January 7, 2020. With the first case reported in Thailand about a week later, the virus’s spread outside the borders of China became apparent. In an alarmingly short time, the new type of coronavirus disease (called COVID-19) started to gain worldwide recognition with the detection of various COVID-19 cases in multiple countries, including Japan, South Korea, USA, Singapore, France, Germany, Italy, Spain, and England. As a result of its rampant spread and fatal clinical manifestations, the coronavirus outbreak was declared a pandemic on March 11, 2020, by the World Health Organization (WHO). Turkey announced its first confirmed case of COVID-19 on the same date that WHO characterized COVID-19 as a pandemic. As of April 2020, the COVID-19 pandemic has traveled to 209 countries and territories around the world, infecting more than 3 million people. Since specific treatment and vaccine for COVID-19 are not yet available, early case detection and preventive healthcare practices (isolation, social distancing, and personal hygiene) play a critical role in combating the COVID-19 outbreak. This review is intended to build an overall picture of the COVID-19 outbreak based on the available scientific knowledge.Article Citation - WoS: 6Citation - Scopus: 8A “sweet” Way To Increase the Metabolic Activity and Migratory Response of Cells Associated With Wound Healing: Deoxy-Sugar Incorporated Polymer Fibres as a Bioactive Wound Patch(TÜBİTAK, 2022) Dikici, SerkanThe selection of a wound dressing is crucial for successful wound management. Conventional dressings are preferable for the treatment of simple wounds. However, a bioactive wound dressing that supports wound management and accelerates the healing process is required when it comes to treating non-self-healing wounds. 2-deoxy-D-ribose (2dDR) is a small deoxy sugar that naturally occurs in human body. Although we have previously demonstrated that 2dDR can be used to induce neovascularisation and accelerates wound healing in vitro and in vivo, the literature on small sugars is conflicting, and the knowledge on how 2dDR achieves its biological activity is very limited. In this study, several small sugars including D-glucose (DG), 2-deoxy-D-glucose (2dDG), 2deoxy-L-ribose (2dLR) were compared to 2dDR by investigating their effects on the metabolic activities of both human dermal microvascular endothelial cells (HDMECs) and human dermal fibroblasts (HDFs). Then, for the first time, a two-dimensional (2D) scratch wound healing model was used to explore the migratory response of HDFs in response to 2dDR treatment. Finally, 2dDR was incorporated into Poly(3-hydroxybutyrate-co3-hydroxyvalerate) (PHBV) polymer fibres via electrospinning, and the metabolic activity of both types of cells in vitro was investigated in response to sugar release via Alamar Blue assay. The results demonstrated that 2dDR was the only sugar, among others, that enhances the metabolic activity of both HDMECs and HDFs and the migratory response of HDFs in a 2D scratch assay in a dose-dependent manner. In addition to direct administration, 2dDR was also found to increase the metabolic activity of HDMECs and HDFs over 7 days when released from polymer fibres. It is concluded that 2dDR is a potential pro-angiogenic agent that has a positive impact not only on endothelial cells but also fibroblasts, which take a key role in wound healing. It could easily be introduced into polymeric scaffolds to be released quickly to enhance the metabolic activity and the migratory response of cells that are associated with angiogenesis and wound healing.Article Lif Kabağı Takviye Edilmiş Kitosan-ipek Hidrojel Kompozit Doku İskelelerinin Kıkırdak Doku Hasarı Tedavisinde Kullanımının Araştırılması(2021) Çolpankan Güneş, Oylum; Özer, İbrahim Erkut; Kara, Aylin; Ziylan Albayrak, Aylin; Havıtçıoğlu, HasanKıkırdak doku hasarlarının onarılmasındaki mevcut tedaviler, kıkırdağın kendi kendini iyileştirme kapasitesinin düşük olması nedeni ile sınırlıdır. Son yıllarda doku mühendisliği, kıkırdak rejenerasyonu için umut verici bir yaklaşım olarak önerilmektedir. Bu çalışmada, kıkırdak doku hasarları için lif kabağı ile güçlendirilmiş ipek fibroin/kitosan hidrojeller hazırlanmıştır. Biyouyumlu, biyolojik olarak parçalanabilir ipek fibroin ve kitosan polimerleri, doğal ve toksik olmayan bir çapraz bağlama maddesi olan genipin ile çapraz bağlanmıştır. Taramalı elektron mikroskobu (SEM) ve Fourier Dönüşümü Kızılötesi Spektroskopisi (FTIR) sırasıyla morfoloji ve kimyasal yapı karakterizasyonu için kullanılmıştır. Viskoelastik özelliklerin belirlenmesi için dinamik mekanik analiz cihazı (DMA) kullanılırken, iskelelerin mekanik özelliklerini incelemek için basma testi kullanılmıştır. Doku iskelelerinin sitotoksisitesi, hücre canlılığı ve çoğalması tavşan mezenkimal kök hücreleri kullanılarak LDH, WST ve kollajen testi ile araştırılmıştır. Üretilen hidrojel kompozit doku iskelelerinin tamamının birbirine bağlı mikro gözenekli bir yapıya sahip olduğu ve lif kabaklarının yapıya iyi entegre olduğu görülmektedir. Ağırlıkça %0,3 genipin ile çapraz bağlanan hidrojel kompozit doku iskelesi (L-CSG3), eklem kıkırdağıyla karşılaştırılabilir su içeriği (94,4±% 0,2), tan ? (1 Hz'de 0,18) ve basma modülü (5,5 MPa) değerleri göstermiştir. Ayrıca, in-vitro test sonuçlarına göre, bu hidrojel kompozit doku iskelesi, tavşan mezenkimal kök hücrelerinde gelişmiş canlılık göstermiştir. Sonuç olarak, bu hidrojel kompozit doku iskelesi, kıkırdak dokusu rejenerasyonu için umut vaat ettiği söylenebilir.Article Citation - WoS: 6Citation - Scopus: 6Benzodiazepine Derivatives From Marine-Derived Streptomyces Cacaoi 14cm034(ACG Publications, 2021) Çetinel Aksoy, Semiha; Küçüksolak, Melis; Uzel, Ataç; Bedir, Erdal7-methoxy-8-hydroxy cycloanthranilylproline (2), a new natural product with pyrrolobenzodiazepine (PBD) framework, was isolated from marine-derived actinobacterium Streptomyces cacaoi 14CM034, together with cycloanthranilylproline (1). Structural elucidation of the compounds was based on FTIR, 1D-(H-1 and C-13 NMR), 2D-NMR (COSY, HMBC and NOESY) and HR-MS analyses. Compounds 1 and 2 exhibited notable antimicrobial activity. The presence of PBD derivatives in S. cacaoi was first demonstrated with this study.Article Citation - WoS: 8Citation - Scopus: 12Adjuvant Potency of Astragaloside Vii Embedded Cholesterol Nanoparticles for H3n2 Influenza Vaccine(TÜBİTAK, 2020) Genç, Rukan; Yakuboğulları, Nilgün; Nalbantsoy, Ayşe; Coven, Fethiye; Bedir, ErdalAdjuvants are substances that increase the immune response to a given antigen. In the development of novel vaccine adjuvants/systems, saponins are one of the most attractive molecules due to their altered immunomodulatory activities. In this study, we tried to develop PEG (polyethylene glycol)/cholesterol-based lipid nanoparticles (LNPs) to deliver the Astragaloside VII (AST-VII) and potentiate adjuvant properties of AST-VII for the influenza vaccine. In the formation of PEG/cholesterol/AST-VII-based LNPs (PEG300: Chol-AST-VII LNPs), 3 different primary solvents (acetone, ethanol, and chloroform) were evaluated, employing their effects on hydrodynamic particle size, distribution, surface chemistry, and colloidal stability. Prepared nanoparticles were simply admixtured with inactivated influenza antigen (H3N2) and applied to PMA (phorbol 12-myristate 13-acetate)-ionomycin treated human whole blood to evaluate their cytokine release profile. PEG300: Chol-AST-VII LNPs (80.2 +/- 7.7 nm) were obtained using chloroform as a desolvation agent. Co-treatment of PMA-ionomycin with AST-VII and PEG300: Chol-AST-VII LNPs significantly increased the levels of IL-2 and IFN-gamma, compared to PMA-ionomycin alone. In the presence of H3N2, AST-VII was able to augment IL-17A, while PEG300: Chol-AST-VII LNPs stimulated the production of IFN-gamma. Hemolysis was only observed in PEG300: Chol-AST-VII LNPs (250 mu g/mL) treatment. AST-VII and AST-VII-integrated LNPs could be used as efficacious adjuvants for an inactivated H3N2 vaccine in vitro, and cytokine response through Th1/Th17 route was reported.