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    Aptamer decorated PDA@magnetic silica microparticles for bacteria purification
    (Springer Wien, 2024) Kavruk, Murat; Babaie, Zahra; Kibar, Gunes; Cetin, Barbaros; Yesilkaya, Hasan; Amrani, Yassine; Dursun, Ali Dogan
    One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.
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    Assessment of Anticancer Effects of Aloe vera on 3D Liver Tumor Spheroids in a Microfluidic Platform
    (Wiley, 2025) Tevlek, Atakan; Kibar, Gunes; Cetin, Barbaros
    The search for effective anticancer therapies has increasingly focused on natural compounds like Aloe vera, renowned for its therapeutic properties. This study investigates the anticancer properties of Aloe vera on 3D liver tumor spheroids via a PDMS-based microfluidic device, providing a more physiologically realistic model compared to traditional 2D cultures. HepG2 cells were cultivated to generate 3D spheroids on-chip, thereafter subjected to different concentrations of Aloe vera and the chemotherapeutic drug Doxorubicin to evaluate cytotoxic effects. The microfluidic system, validated by COMSOL simulations, facilitated continuous perfusion and real-time assessment of cell viability over a duration of 10 days. The results indicated that Aloe vera markedly diminished cell viability by triggering apoptosis at concentrations over 12.5 mg/mL. IC50 values were determined at 72 h: 25 +/- 0.10 mg/mL for Aloe vera and 5.47 +/- 0.03 mu g/mL for Doxorubicin in 2D cultures, but in 3D cultures, the IC50 values were 31.25 +/- 0.14 mg/mL for Aloe vera and 8.33 +/- 0.05 mu g/mL for Doxorubicin. This study underscores the promise of Aloe vera as a natural anticancer agent and illustrates the efficacy of microfluidic platforms for enhanced drug screening and customized medicine applications.
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    Microfluidic rapid isolation and electrochemical detection of S. pneumonia via aptamer-decorated surfaces
    (Elsevier, 2025) Babaie, Zahra; Kibar, Gunes; Yesilkaya, Hasan; Amrani, Yassine; Dogan, Soner; Tuna, Bilge G.; Ozalp, Veli C.; Cetin, Barbaros
    Background: S. pneumoniae is widely recognized as a leading cause of respiratory infections worldwide, often resulting in high mortality rates. However, the advent of microfluidic technologies has brought significant advancements, including the simplified, sensitive, cost-effective, and rapid approach to pneumococcal bacteremia detection. In this study, a microfluidic magnetic platform is presented for rapid isolation, and an electrode array is utilized for the electrochemical detection of S. pneumoniae. Aptamer-decorated surfaces were employed for both isolation and detection. For isolation, silica magnetic microparticles were synthesized and decorated with aptamer. Results: Isolation performance was assessed for phosphate-buffered saline (PBS) and blood samples for different concentrations of S. pneumoniae. Electrical impedance spectroscopy (EIS) with fabricated gold interdigitated electrodes (IDEs) decorated with aptamer was implemented for the detection of S. pneumoniae at different bacteria concentrations. The microfluidic platform performed bacteria isolation at comparable isolation efficiency with batch systems but at a much faster rate (isolation took about a minute, and the aptamer-decorated electrode array exhibited a limit of detection (LOD) at 962 CFU/mL and linear range between 104 and 107CFU/mL. Significance: Our method represents a significant advancement compared to previous reports. Our microfluidic platform can efficiently isolate 60 mu L of the bacteria sample within about one minute. The entire process takes about two minutes including the detection step. Furthermore, our method achieves a notable improvement in the detection limit for S. pneumoniae compared to conventional ELISA and magnetic microfluidics ELISA.
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    Microfluidic vs. batch synthesis of fluorescent poly(GMA-co-EGDMA) micro/nanoparticles for biomedical applications
    (Springernature, 2024) Kilincli, Betul; Cinar, Ayse Duru; Cetin, Barbaros; Kibar, Gunes
    Fluorescent particles play a crucial role in nanomedicine and biological applications such as imaging, diagnostic tools, drug delivery, biosensing, multimodal imaging, and theranostics. This report presents a novel synthesis method and comparative study for synthesizing fluorescent particles in microfluidic continuous and batch-type reactors. Glycidyl methacrylate (GMA) and ethylene glycol dimethyl acrylate (EGDMA) are well-known monomers for synthesizing functional particles for biomedical applications. Several methods exist to obtain fluorescent poly(GMA-co-EGDMA) (p(GMA-EGDMA))particles through various polymerization techniques. Unlike existing methods, we developed a green approach for synthesizing fluorescent p(GMA-EGDMA) particles via UV-initiated one-step emulsion polymerization by comparing microfluidic and batch synthesis. Moreover, as a fluorescent dye, fluorescein isothiocyanate (FITC) was directly incorporated with p(GMA-EGDMA) particles at various concentrations to achieve tunable fluorescent functionality. While the batch synthesis resulted in polydisperse fluorescent p(GMA-EGDMA)microparticles with spherical shapes ranging from 25 mu m to 1.0 mu m in size, the microfluidic synthesis produced nonspherical nanoparticles. Fluorescent FITC@p(GMA-EGDMA) particles were characterized by scanning electron microscope (SEM), fluorescent microscope, and Fourier-transform infrared spectroscopy (FTIR). The synthesized particles have potential for fluorescence imaging applications, specifically bio-detection in array systems.
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    Novel 3D-Printed Microfluidic Magnetic Platform for Rapid DNA Isolation
    (Amer Chemical Soc, 2024) Kibar, Gunes; Sariarslan, Busra; Doganay, Serkan; Yildiz, Gokay; Usta, O. Berk; Cetin, Barbaros
    This study presents a novel miniaturized device as a 3D-printed microfluidic magnetic platform specifically designed to manipulate magnetic microparticles in a microfluidic chip for rapid deoxyribonucleic acid (DNA) isolation. The novel design enables the movement of the magnetic particles in the same or opposite directions with the flow or suspends them in continuous flow. A computational model was developed to assess the effectiveness of the magnetic manipulation of the particles. Superparamagnetic monodisperse silica particles synthesized in-house are utilized for the isolation of fish sperm DNA and human placenta DNA. It was demonstrated that the proposed platform can perform DNA isolation within 10 min with an isolation efficiency of 50% at optimum operating conditions.
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    One-pot synthesis of organic-inorganic hybrid polyhedral oligomeric silsesquioxane microparticles in a double-zone temperature controlled microfluidic reactor
    (Wiley, 2019) Kibar, Gunes; Caliskan, Umutcan; Erdem, E. Yegan; Cetin, Barbaros
    Polyhedral oligomeric silsesquioxane (POSS) particles are one of the smallest organosilica nano-cage structures with high multifunctionality that show both organic and inorganic properties. Until now poly(POSS) structures have been synthesized from beginning with a methacryl-POSS monomer in free-radical mechanism with batch-wise methods that use sacrificial templates or additional multisteps. This study introduces a novel one-pot synthesis inside a continuous flow, double temperature zone microfluidic reactor where the methodology is based on dispersion polymerization. As a result, spherical monodisperse POSS microparticles were obtained and characterized to determine their morphology, surface chemical structure, and thermal behavior by SEM, FTIR, and TGA, respectively. These results were also compared and reported with the outcomes of batch-wise synthesis. (c) 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1396-1403