Yücesoy, Deniz Tanıl
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Yucesoy, D. T.
Yücesoy, Deniz T.
Yucesoy, Deniz T.
Yucesoy, Deniz Tanil
Yücesoy, Deniz T.
Yucesoy, Deniz T.
Yucesoy, Deniz Tanil
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denizyucesoy@iyte.edu.tr
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03.01. Department of Bioengineering
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10
Citations
199
Scholarly Output
9
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3
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7676/1590
Supervised MSc Theses
5
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32
Scopus Citation Count
36
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3.56
Scopus Citations per Publication
4.00
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6
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5
| Journal | Count |
|---|---|
| ACS Biomaterials Science and Engineering | 1 |
| ACS Omega | 1 |
| JOM | 1 |
| Toxicology Letters | 1 |
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9 results
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Now showing 1 - 9 of 9
Article Citation - Scopus: 1Investigating Early-Stage Mineralization Behavior and Bioactivity of Acid-Free Bioactive Glass 45s5 With Enhanced Dissolution Kinetics(Springer, 2025) Tuncer, Melisa; Yucesoy, Deniz T.; Karakus, Ceyda OkselNanostructured bioactive glass (BG) was synthesized through an acid-free sol-gel route (bioglass-AF) and the conventional acid-catalyst sol-gel process (bioglass-AC). The aim here is to eliminate the risk of residual acidic components in the BG while enhancing its functionality through nano-scale propduction. Scanning electron microscopy revealed the presence of highly porous structures and dense agglomerates composed of particles with a mean diameter of 45 nm in both samples. Bioglass-AC and bioglass-AF had specific surface areas of 1.48 m(2)/g and 2.73 m(2)/g, respectively, with an average pore size of similar to 5 nm. Faster mineralization kinetics were evident in bioglass-AF, compared to bioglass-AC, in Hepes-buffered salt solution. Following 14 days of immersion in artificial saliva, bioglass-AC and bioglass-AF lost 16% and 20% of their initial weight, respectively, confirming their bioactivity. None of the synthesized BGs stimulated cell growth up to 24 h but longer exposure to moderate concentrations (1.25 and 2.5 mg/mL) of bioglass-AF significantly enhanced cell viability, reaching 170% at 48 h. Overall, the comparative in vitro investigations proved that nano-structured 45S5 bioglass powders with improved mineralization and dissolution kinetics can be produced with an acid-free route, eliminating the risk of residual acidic components in the final product.Master Thesis In Silico Design of Chimeric Peptides for Infection Resistant Implant Coatings(01. Izmir Institute of Technology, 2023) Kan, İlker; Yücesoy, Deniz Tanıl; Özçivici, EnginTooth loss has been a widespread dental problem affecting patients of various ages. Replacement of lost teeth with implants is a common practice for managing tooth loss due to their mechanical properties and natural-looking aesthetics. One of the persistent problems associated with dental implants is the risk of infection (periimplantitis) which can occur when bacteria colonize the implant surface leading to inflammation and tissue damage with an eventual implant failure. Infection-resistant antimicrobial coatings have been one of the promising solutions to combat implant infections. The purpose of this study was to design functional chimeric peptides using antimicrobial peptides and hydroxyapatite binding peptides in order to provide an antimicrobial effect to hydroxyapatite-coated titanium dental implants. For this purpose, since titanium implants coated with hydroxyapatite show long-term biocompatibility, chimeric peptides that can provide antimicrobial resistance have been designed by considering antimicrobial peptides in addition to these coatings. Computational analysis, solubility analysis, secondary structure analysis, and conformational change analysis were performed to examine the ability of these formed chimeric peptides to retain their antimicrobial properties. Promising candidates obtained from secondary structure analysis and solubility analysis were examined to preserve their structure and stability by performing conformational change analysis, and the most suitable candidates were decided. Although the results give candidates computationally according to the analysis, these candidates should be confirmed experimentally. When the results from the computational analysis are validated by the experimental analysis, it will set the standard for antimicrobial chimeric peptide design.Article Citation - WoS: 13Citation - Scopus: 13Solid-Binding Peptide-Guided Spatially Directed Immobilization of Kinetically Matched Enzyme Cascades in Membrane Nanoreactors(American Chemical Society, 2021) Yücesoy, Deniz Tanıl; Akkineni, Susrut; Tamerler, Candan; Hinds, Bruce J.; Sarıkaya, MehmetBiocatalysis is a useful strategy for sustainable green synthesis of fine chemicals due to its high catalytic rate, reaction specificity, and operation under ambient conditions. Addressable immobilization of enzymes onto solid supports for one-pot multistep biocatalysis, however, remains a major challenge. In natural pathways, enzymes are spatially coupled to prevent side reactions, eradicate inhibitory products, and channel metabolites sequentially from one enzyme to another. Construction of a modular immobilization platform enabling spatially directed assembly of multiple biocatalysts would, therefore, not only allow the development of high-efficiency bioreactors but also provide novel synthetic routes for chemical synthesis. In this study, we developed a modular cascade flow reactor using a generalizable solid-binding peptide-directed immobilization strategy that allows selective immobilization of fusion enzymes on anodic aluminum oxide (AAO) monoliths with high positional precision. Here, the lactate dehydrogenase and formate dehydrogenase enzymes were fused with substrate-specific peptides to facilitate their self-immobilization through the membrane channels in cascade geometry. Using this cascade model, two-step biocatalytic production of l-lactate is demonstrated with concomitant regeneration of soluble nicotinamide adenine dinucleotide (NADH). Both fusion enzymes retained their catalytic activity upon immobilization, suggesting their optimal display on the support surface. The 85% cascading reaction efficiency was achieved at a flow rate that kinetically matches the residence time of the slowest enzyme. In addition, 84% of initial catalytic activity was preserved after 10 days of continuous operation at room temperature. The peptide-directed modular approach described herein is a highly effective strategy to control surface orientation, spatial localization, and loading of multiple enzymes on solid supports. The implications of this work provide insight for the single-step construction of high-power cascadic devices by enabling co-expression, purification, and immobilization of a variety of engineered fusion enzymes on patterned surfaces. © 2021 The Authors. Published by American Chemical Society.Master Thesis Green Synthesis of Nanostructured Bioactive Glass for Dental Applications(01. Izmir Institute of Technology, 2023) Tüncer, Melisa; Yücesoy, Deniz Tanıl; Öksel Karakuş, CeydaBioactive glass is a biomaterial commonly used in dental care products and bone tissue engineering applications due to its biocompatibility, bone-forming ability, and remineralization capability. Bioactive glasses form a hydroxyapatite-like layer on dentinal tubules by releasing calcium and phosphorus ions after interaction with saliva. Bioactive 45S5 glass traditionally synthesized by wet chemical methods which require high-temperature heating and the use of a strong acid catalyst, bringing into question of the possibility of introducing toxic acid residues into the final product. Therefore, there is a need to develop environmental-friendly bioactive glass synthesis methods or to modify existing ones in a way to uplift their environmental friendliness. To satisfy this need, we greenized the traditional sol-gel method by replacing the acid catalyst with an environment-friendly alternative and successfully used it for the synthesis of nanostructured 45S5 bioactive glass. First, physicochemical characterization of the synthesized bioactive glasses was performed. Then, the apatite formation capability of bioglasses were investigated in saliva. Next, the mineralization kinetics of bioglasses were tested in Ca/P buffer. In vitro toxicity tests were performed to assess the cytotoxic potential of the synthesized bioactive glass. All analyses were repeated for the traditional synthesis method for comparison purposes. The results confirmed that green synthesis is more advantageous in terms of bioactivity and functionality required for dental applications. Increasing the safety and functionality of bioglass at the same time during the production phase has critical importance for ensuring the sustainability of current applications as well as creating new uses in the biomedical fieldMaster Thesis The Morphology and Kinetics Control of Calcium Phosphate Mineralization Using Tiny Enzymes Identified Through Deep-Directed Evolution(01. Izmir Institute of Technology, 2024) Çelik, Nursevim; Yücesoy, Deniz TanılBiyomineralizasyon çeşitli organizmalarda inorganik iyonların organik protein molekülleri ile birlikte koordineli bir şekilde çökelmesine ve büyümesine rehberlik eden temel biyolojik olgudur. İnsanlar başta olmak üzere omurgalılarda kemik ve diş omurgasızlarda yumuşakçaların kabukları gibi sert dokularının oluşumu biyomineralizasyonun bir parçasıdır. Biyomineralizasyonun etkili yönetimi, vasküler kalsifikasyon gibi istenmeyen oluşumları önlemek ve kemik ve diş remineralizasyonu gibi faydalı süreçleri teşvik etmektir. Biyomineralizasyonunda yer alan moleküler mekanizmaların ve düzenleyici yolların anlaşılması, tıbbi ve dental araştırmaların, terapötik müdahalelerin ve biyomimetik materyal tasarımının ilerletilmesi için gereklidir. Bu sürecin temeli, belirli özelliklere ve işlevlere sahip mineral malzemelerin oluşumunun morfolojisinin ve kinetiğinin hassas bir şekilde kontrol edilmesini içerir. Bu tez, derin yönlendirmeli evrim yoluyla tanımlanan küçük enzimler kullanarak kalsiyum fosfat mineralizasyonunun morfolojisini ve kinetiğini kontrol etmeyi amaçlamaktadır. Kalsiyum fosfat minerallerinin mineralizasyon kinetiğini ve morfolojisini önemli ölçüde yönlendirerek kontrol eden kısa dizili peptitleri (12 amino asit) fizyolojik bir ortamdan seçmek için bir peptit-faj kütüphanesi kullanılmıştır. Mineralizasyon süreci üzerindeki dinamik etkileri bilinen, pH, sıcaklık ve molarite gibi değişkenlerin mineralizasyon için en uygun koşulları yinelemeli deneylerle ayarlanmıştır. Bu peptitlerin varlığında hidroksiapatit kristallerinin oluşumu yapısal karakterizasyon için kullanılan SEM, XRD ve FTIR analizleri ile kanıtlanmıştır. Kinetik ölçümler, bu peptitlerin fizyolojik koşullar altında kalsiyum fosfat mineralizasyonunu yaklaşık bir kat daha hızlı katalize ettiği kinetik ölçümler ile ortaya koymuştur. Mineral kristalleri üzerinde etkisi doğrulanan bu peptitler diş jelleri, diş macunu formülasyonları ve kemik rejenerasyonu tedavileri gibi klinik ürünlerin geliştirilmesi için potansiyel taşımaktadır.Conference Object Citation - WoS: 1Green Synthesis of Nanostructured Bioactive Glass for Dental Applications(Elsevier, 2022) Tüncer, Melisa; Yücesoy, Deniz Tanıl; Öksel Karakuş, CeydaCalcium sodium phosphosilicate (known as bioactive glass) is a biomaterial commonly used in dental care products and bone tissue engineering applications due to biocompatibility, bone-forming and dentin sensitivity reduction capability. Bioactive 45S5 glass, so-called NovaMin, comprises of 45% SiO2, 24.5% Na2O, 24.5% CaO, and 6% P2O5 (wt%). It is traditionally synthesized by wet chemical methods such as melt-quenching and sol-gel which requires high temperature heating and the use of a strong acid catalyst, which brings into the question of the possibility of introducing toxic acid residues into the final product. Therefore, there is a clear need to develop environmental-friendly bioactive glass synthesis methods or to modify existing ones in a way to uplift their environmental friendliness.Master Thesis High-Throughput Selection of Mineralizing Peptides(01. Izmir Institute of Technology, 2024) Çulha, Gizem; Toptan, Fatih; Yücesoy, Deniz Tanıl3,4 milyar yılı aşkın protein evrimi boyunca Doğa Ana, biyomineral oluşumunu düzenleyen ve kontrol eden moleküler yollar geliştirmiştir. Biyolojik sert dokuların mükemmel hiyerarşik yapıları ve çok işlevli özellikleri uzun süredir malzeme bilimcilerine ve mühendislerine ilham kaynağı olmuştur. Proteinler tarafından sentezlenen bu doğal kompozitler, inorganik katıların çekirdeklenmesini ve büyümesini kolaylaştırır ve böylece organizmalarda mineral oluşumunu yönlendirir. Biyomineralizasyon yaşam için gerekli olmasına rağmen; düzensizliği önemli sağlık sorunlarına yol açabilir. Bu nedenle, bu mekanizmayı anlamak anormal mineral birikimiyle ilişkili hastalıklara yönelik tedavilerin geliştirilmesi açısından çok önemlidir. Nano ölçekte biyolojiden ilham alan bu tezin amacı, derin yönelimli evrim yaklaşımıyla doğal proteinlere benzer şekilde hidroksiapatit (HAp) mineralizasyonunu yönetebilen kısa katalitik peptitleri tanımlamaktır. Sonuçlarımız, benzersiz dizilere sahip peptitlerin tanımlandığını gösterdi. XRD ve FTIR analizleri yoluyla yapılan yapısal karakterizasyon, bu peptitlerin varlığında hidroksiapatit oluşumunu doğruladı. Bununla birlikte, kinetik ölçümler bu peptitlerin fizyolojik koşullar altında kalsiyum fosfat mineralizasyonunu on beş kat daha hızlı katalize ettiğini ortaya çıkardı. Bu peptitlerin, kalsiyum ve fosfat ile desteklenmiş sulu ortamda sergilediği hızlı mineralizasyon kinetiği, demineralize olmuş dokuların onarılması ve patolojik biyomineralizasyon ile ilişkili hastalıkların tedavisi için güçlü bir potansiyele işaret etmektedir. Aynı zamanda, bu peptit dizileri, diş jelleri ve diş macunu formülasyonları dahil olmak üzere klinik ürünlerin geliştirilmesinde, kemik rejenerasyonu tedavilerinde ve kontrollü mineralizasyonun önemli olduğu diğer tıbbi uygulamalarda temel unsurlar olarak hizmet edebilirMaster Thesis Machine-learning-assisted de novo design of molybdenum disulfide binding peptides(01. Izmir Institute of Technology, 2024) Öğüt, Alp Deniz; Yücesoy, Deniz Tanıl; Apaydın, Mehmet SerkanKısa amino asit zincirleri, peptitler, biyolojik süreçler ve yüksek teknoloji uygulamaları için vazgeçilmez moleküllerdir. Geniş kullanım alanları arasında, moleküler tanıma özelliği ile bio-nano arayüzler oluşturmak ilgi toplayan bir araştırma konusu olmuştur. Yapılan çalışmalar sonucunda yönlendirilmiş evrim metodolojileri oluşturulmuş ve çeşitli hedeflere -enzim, antijen veya inorganik yapılar- bağlanan fonksiyonel peptit tanısı mümkün hale gelmiştir fakat bu geleneksel yaklaşım ölçeklenebilirlik ve sekans uzayındaki ilişkilerin anlaşılması konusunda zayıflıklar taşımaktadır. Bu zafiyetler, yüksek çıktılı sekanslama ve hesaplama verimlerinin artması ile beraber derin yönlendirilmiş evrim gibi daha güçlü teknolojilerinin geliştirilmesini motive etmiştir. Bu yöntemle üretilen büyük veri setleri, sekans-fonksiyon ilişkilerinin makine öğrenmesi ile modellenebilmesinin önünü açmıştır. Bu tezin amacı bu veri setlerine uygun bir makine öğrenmesi akışı oluşturmaktır. Bu düzlemde Random Forest algoritması ve derin nöral ağlar kullanılmış, eğitilen modellerin bağlanma puanı öngörüleri beraber kullanıldığında mutlak hata sırasıyla, 0.0304, Pearson korelasyon ölçütü 0.904 olarak elde edilmiştir. Bu modelleri kullanarak rastgele arama ve tekrarlayan optimizasyonlar ile güçlü bağlanan örnek bir peptit tasarlanmıştır. Bulgular alan bilgisinin makine öğrenme modeli eğitimdeki yerini vurgulamış, kullanılan örnek ağırlıklarının ve semantik amino asit vektörlerinin başarıya önemli katkıları gözlemlenmiştir. Bu çalışma çeşitli fonksiyonlara sahip peptit tasarlayabilen bir platform oluşturabilmek için temel noktaları göz önüne serer.Article Citation - WoS: 18Citation - Scopus: 22Biomimetic Dentin Repair: Amelogenin-Derived Peptide Guides Occlusion and Peritubular Mineralization of Human Teeth(American Chemical Society, 2023) Fong, Hanson; Hamann, John; Hall, Eric; Yücesoy, Deniz T.; Doğan, Sami; Sarıkaya, MehmetExposure of dentin tubules due to loss of protective enamel (crown) and cementum (root) tissues as a result of erosion, mechanical wear, gingival recession, etc. has been the leading causes of dentin hypersensitivity. Despite being a widespread ailment, no permanent solution exists to address this oral condition. Current treatments are designed to alleviate the pain by either using desensitizers or blocking dentin tubules by deposition of minerals or solid precipitates, which often have short-lived effects. Reproducing an integrated mineral layer that occludes exposed dentin with concomitant peritubular mineralization is essential to reestablish the structural and mechanical integrity of the tooth with long-term durability. Here, we describe a biomimetic treatment that promotes dentin repair using a mineralization directing peptide, sADP5, derived from amelogenin. The occlusion was achieved through a layer-by-layer peptide-guided remineralization process that forms an infiltrating mineral layer on dentin. The structure, composition, and nanomechanical properties of the remineralized dentin were analyzed by cross-sectional scanning electron microscopy imaging, energy dispersive X-ray spectroscopy, and nanomechanical testing. The elemental analysis provided calcium and phosphate compositions that are similar to those in hydroxyapatite. The measured average hardness and reduced elastic modulus values for the mineral layer were significantly higher than those of the demineralized and sound human dentin. The structural integration of the new mineral and underlying dentin was confirmed by thermal aging demonstrating no physical separation. These results suggest that a structurally robust and mechanically durable interface is formed between the interpenetrating mineral layer and underlying dentin that can withstand long-term mechanical and thermal stresses naturally experienced in the oral environment. The peptide-guided remineralization procedure described herein could provide a foundation for the development of highly effective oral care products leading to novel biomimetic treatments for a wide range of demineralization-related ailments and, in particular, offers a potent long-term solution for dentin hypersensitivity.