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Sözmen, Alper Baran
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01. Izmir Institute of Technology
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7
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4
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58600/1276
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16
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29
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2
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2.29
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4.14
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3
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1
| Journal | Count |
|---|---|
| Biosensors and Bioelectronics: X | 2 |
| 43rd FEBS Congress, Biochemistry Forever | 1 |
| Biocatalysis and Agricultural Biotechnology | 1 |
| FEBS Open Bio | 1 |
| Microfluidics and Nanofluidics | 1 |
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Now showing 1 - 7 of 7
Conference Object Immobilized Gold Nanoparticle Based Plasmonic Assay Platform for Biomolecule and Microorganism Detection(Wiley, 2021) Sözmen, Alper Baran; Sözmen, Alper Baran; Arslan Yıldız, Ahu; Arslan Yıldız, Ahu; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringPlasmonic sensors are suitable tools for study of molecular interactions. Localized Surface Plasmon Resonance (LSPR) based sensors detect spectral changes associated with intramolecular interactions between analyte molecules and recognition elements. Due to its labelfree and highly sensitive features, LSPR based methods have high potential for biosensing applications. In this study, we aim to develop a sensitive, labelfree, rapid and simple biosensing platform. For this purpose, a novel refractive index (RI) sensitivity enhancement methodology is proposed by immobilizing gold nanoparticles (GNPs) for platformbased LSPR. Fabrication of platform was carried out by GNP synthesis, immobilization of GNPs on polystyrene solid support, and growth of GNPs. Validation of response to RI changes of developed sensor platform was carried out by tests with varying concentrations of sucrose and ethanol. Then as a proofofconcept, detection ability and detection limit determination of E.coli BL21 (DE3) and protein Bovine Serum Albumin (BSA) was carried out. Adsorption of E.coli BL21 (DE3) via bulk interactions showed that the developed LSPR platform exhibit high enough binding affinity for bacteria detection, and was able to detect down to concentrations as low as 102 CFU/ml. Immune capturing of BSA via antiBSA antibody showed that the developed LSPR platform was able to detect BSA protein–antibody interaction down to 10 µM concentration range.Conference Object Evaluation of Anti-Inflammatory Potential and Lc-ms/Ms Analysis of Different Standards(Wiley, 2018) Sözmen, Alper Baran; Sözmen, Alper Baran; Canbay, E.; Yıldırım Sözmen, Eser; Övez, Bikem; 01. Izmir Institute of TechnologyStandardization of a LC-MS/MS method for phenolic compound content of biomass originated extracts was aimed in this study, Chlorella miniata extracts, which were cultivated solely for this study, were used for this purpose. The first step of the study was to compare external standard method, added standard method, and conventional standard method the qualitative identification of phenolic compounds of the extracts were performed by using LC-MS/MS system.Doctoral Thesis Development of Optical Sensor Platforms for Exosome Detection(01. Izmir Institute of Technology, 2024) Sözmen, Alper Baran; Arslan Yıldız, Ahu; Sözmen, Alper Baran; Yıldız, Ahu Arslan; Akan, Pınar; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringBu tez, eksozom tespiti için optik sensör platformlarının kullanılması yoluyla kanserin erken teşhisi ve izlenmesi için yeni bir yaklaşım önermektedir. Kanser prognozu, teşhisi ve izlenmesine yönelik mevcut teknolojiler, özellikle erken evrelerdeki etkinlikleri ve invazivlikleri açısından önemli sınırlamalarla karşı karşıyadır. Bu zorlukların üstesinden gelmek için bu çalışma, iyi tanımlanmış membran protein profili nedeniyle Küçük Hücreli Dışı Akciğer Kanserine (NSCLC) vurgu yaparak, kanserli ekzozomal membran proteinlerini tespit edebilen gelecekteki sıvı biyopsi uygulamaları için biyosensör platformları geliştirmeye odaklanmaktadır. Araştırma, lokalize yüzey plazmon rezonansı (LSPR) ve manyetik kaldırma (MagLev) prensiplerini kullanan iki optik biyosensör platformunun üretimini, optimizasyonunu ve karakterizasyonunu içermektedir. Biyosensör platformları başlangıçta bir model protein olan Bovine Serum Albumin (BSA) ve sonrasında EpCAM, CD151 ve CD81 Eksozomal Membran Proteinleri (ExoMP'ler) ile test edilmiştir. Bu Sırasıyla eksozomal kanser biyobelirteçleri, eksozomal NSCLC biyobelirteçleri ve eksozomal biyobelirteçler olarak yaygın şekilde kullanıldıkları için bu ExoMP'ler hedef olarak seçilmiştir. A549 NSCLC ve MRC5 sağlıklı akciğer fibroblast hücre hatları, geliştirilen optik biyosensör platformlarının eksozom algılama, tanıma ve miktar belirleme yeteneklerini analiz etmek için in-vitro eksozom kaynakları olarak kullanılmıştır. Her iki platform da kanserden türetilen eksozomları sağlıklı eksozomlardan istatistiksel anlamlılıkla başarılı bir şekilde ayırt edebilmiştir. Genel olarak, bu araştırma, sıvı biyopsi teknikleri yoluyla erken teşhis ve izleme için umut verici bir yaklaşım sağlayarak kanser teşhisi ve kişiselleştirilmiş tıbbın ilerlemesine katkıda bulunmaktadır. Geliştirilen platformlar, daha fazla geliştirme ve araştırma ile kanser prognozu ve teşhisine katkıda bulunma potansiyeline sahiptir.Article Citation - WoS: 8Citation - Scopus: 11Cost-Effective and Rapid Prototyping of Pmma Microfluidic Device Via Polymer-Assisted Bonding(Springer, 2021) Sözmen, Alper Baran; Sözmen, Alper Baran; Arslan Yıldız, Ahu; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringMicrofluidic systems are relatively new technology field with a constant need of novel and practical manufacturing materials and methods. One of the main shortcomings of current methods is the inability to provide rapid bonding, with high bonding strength, and sound microchannel integrity. Herein we propose a novel method of assembly that overcomes the mentioned limitations. Polymer-assisted bonding is a novel, rapid, simple, and inexpensive method where a polymer is solubilized in a solvent and the constituted solution is used as a bonding agent. In this study, we combined this method with utilization of several phase-changing materials (PCMs) as channel-protective agents. Glauber's salt appeared to be more suitable as a channel-protective agent compared to rest of the salts that have been used in this study. Based on the bonding strength, quality analyses, leakage tests, and SEM imaging, the superior assisting bonding solvent was determined to be dichloromethane with a PMMA concentration of 2.5% (W/V). It showed a bonding strength of 23.794 MPa and a nearly non-visible bonding layer formation of 2.83 mu m in width which is proved by SEM imaging. The said combination of PCM, solvent, and polymer concentration also showed success in leakage tests and an application of micro-droplet generator fabrication. The application was carried out to test the applicability of developed prototyping methodology, which resulted in conclusive outcomes as the droplet generator simulation run in COMSOL Multiphysics version 5.1 software. In conclusion, the developed fabrication method promises simple, rapid, and strong bonding with sharp and clear micro-channel engraving.Article Citation - WoS: 8Citation - Scopus: 9Optimization of the Algal Species Chlorella Miniata Growth: Mathematical Modelling and Evaluation of Temperature and Light Intensity Effects(Elsevier, 2022) Sözmen, Alper Baran; Sözmen, Alper Baran; Övez, Bikem; 01. Izmir Institute of TechnologyGrowth of Chlorella miniata, a green microalga was investigated during this study under various temperature and light intensity values with the purpose of determining growth rate changes of the microalgae with cultivation parameters, experiments were carried out using airlift photobioreactors with a study volume of 6 L. Culturing conditions were between 66 and 385 μmol photon m−2 s−1 and between 14 and 30 °C for light intensity and ambient temperature, respectively. Acquired data were then used to test various mathematical models for coherency with experimental results. Aiba Model for light intensity and Skewed Normal Distribution Model for temperature parameters performed superior compared to the rest of the mathematical models used during the study. Utilizing both mathematical models a novel model was deduced to express effects of both light intensity and temperature parameters in combination on algal growth. Then the developed model was used to calculate the optimum growth condition of the species. The proposed mathematical model showed good coherency with experimental data and an average relative error of 1.97% for both temperature and light intensity effects on algal growth. The theoretical optimum temperature and light intensity for the maximum specific growth rate were calculated to be 22.43 °C and 291.5 μmol photon m−2 s−1 respectively.Article Citation - Scopus: 6Sensitive and Rapid Protein Assay Via Magnetic Levitation(Elsevier, 2022) Sözmen, Alper Baran; Arslan Yıldız, Ahu; Sözmen, Alper Baran; Arslan Yıldız, Ahu; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringMagnetic levitation (MagLev) is a newly emerging methodology for biosensing that provides a density-based analysis, which is highly sensitive and versatile. In this study, a magnetic levitation based sensor platform was used for protein detection; and sensor platform optimization was performed for both sensitivity and resolution. Bovine Serum Albumin (BSA) was used as a model protein and detection of BSA was carried out by antibody functionalized polystyrene microspheres (PSMs). Various sizes of PSMs were examined and their performances were compared by statistical analyses in terms of limit of detection (LOD), sensitivity, and resolution. Quantification of the protein was done based on the magnetic levitation height differences of antibody functionalized PSMs. For optimization of the methodology, varied PSMs were utilized, and standardization of PSM diameter, concentration of the antibody to be functionalized, and PSM dilution rates were carried out. In conclusion, 20 μm PSMs diluted to 0.005% W/V and functionalized with anti-BSA antibody at a concentration of 28 μg/ml were determined to provide the best resolution for BSA detection. A dynamic range of 100 nM to 1 mM was observed with an LOD value of 4.1 ng/ml. This sensing platform promises a novel approach with a diverse application field and it provides rapid, consistent, and reproducible results with high resolution and sensitivity.Article Citation - Scopus: 3Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform(Elsevier, 2024) Sözmen, Alper Baran; Baştanlar, Yalın; Elveren, Beste; Sözmen, Alper Baran; Erdoğan, Duygu; Yıldız, Ümit Hakan; Mezgil, Bahadır; Arslan Yıldız, Ahu; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu; 01. Izmir Institute of Technology; 04.01. Department of Chemistry; 03.04. Department of Computer Engineering; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 04. Faculty of SciencePlasmonic 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)