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Review Citation - WoS: 26Citation - Scopus: 23Real-Time Biosensing Bacteria and Virus With Quartz Crystal Microbalance: Recent Advances, Opportunities, and Challenges(Taylor & Francis inc, 2023) Bonyadi, Farzaneh; Kavruk, Murat; Ucak, Samet; Cetin, Barbaros; Bayramoglu, Gulay; Dursun, Ali D. D.; Ozalp, Veli C. C.Continuous monitoring of pathogens finds applications in environmental, medical, and food industry settings. Quartz crystal microbalance (QCM) is one of the promising methods for real-time detection of bacteria and viruses. QCM is a technology that utilizes piezoelectric principles to measure mass and is commonly used in detecting the mass of chemicals adhering to a surface. Due to its high sensitivity and rapid detection times, QCM biosensors have attracted considerable attention as a potential method for detecting infections early and tracking the course of diseases, making it a promising tool for global public health professionals in the fight against infectious diseases. This review first provides an overview of the QCM biosensing method, including its principle of operation, various recognition elements used in biosensor creation, and its limitations and then summarizes notable examples of QCM biosensors for pathogens, focusing on microfluidic magnetic separation techniques as a promising tool in the pretreatment of samples. The review explores the use of QCM sensors in detecting pathogens in various samples, such as food, wastewater, and biological samples. The review also discusses the use of magnetic nanoparticles for sample preparation in QCM biosensors and their integration into microfluidic devices for automated detection of pathogens and highlights the importance of accurate and sensitive detection methods for early diagnosis of infections and the need for point-of-care approaches to simplify and reduce the cost of operation.Article Citation - WoS: 23Citation - Scopus: 26Identification of Bacterial Communities of Fermented Cereal Beverage Boza by Metagenomic Analysis(Elsevier, 2022) Ucak, Samet; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Altunbas, Osman; Soyucok, Ali; Sudagidan, MertBacterial microbiota of directly studied and pre-enriched Boza samples were investigated by metagenomic analysis. Virulence gene contents, biofilm formation, antibiotic susceptibility and clonal relationships of enterococci present in pre-enriched Boza samples were determined. Chemical properties of the samples were also investigated. Although directly studied samples showed a dominance by Lactococcus, Lactobacillus, Leuconostoc, and Streptococcus. NGS upon pre-enrichment of the same Boza samples demonstrated a dominance by Lactococcus, Enterococcus, Escherichia/Shigella, Bacillus, and Lactobacillus. All enterococci were identified as Enterococcus faecium and none of them was positive for vanA, vanB, vanC1, vanD, vanE, vanG, agg, gelE, efaAfs, cylA, ace, hyl, cob, cylB, and cylM genes. However, efaAfm, ccf, cpd, and esp genes were detected in the strains. Only one strain formed biofilm and seven strains showed low adherence. E. faecium strains were resistant to rifampin and erythromycin. PFGE revealed 54-100% clonal relationships of E. faecium strains. Percent acidity of Boza samples were 0.14%-0.51%, pH was 3.00-4.07, protein content was 0.35-1.23 mg/100 mg, total sugar content was 9.64-19.21 mg/100 mg Boza, crude ash content was 0.05-0.18 mg/100 mg dry sample, total dry matter was 13.79-28.04 mg/100 mg. Our results indicate to importance of the dynamics nature of microbial communities involved in Boza fermentation and virulence properties of enterococci.Article Citation - WoS: 3Citation - Scopus: 2Targeted Multidrug Delivery Systems To Kill Antibiotic-Resistant Staphylococcus Aureus(Elsevier, 2023) Ozalp, Veli Cengiz; Ucak, Samet; Dursun, Ali D.; Sudagidan, Mert; Icin, Oyku; Vakifahmetoglu, Cekdar; Gurlo, AleksanderDifferent ordered mesoporous silica (OMS) nanoparticles, ranging from regular COK-12 to COK-12 modified in terms of pore shape and size, have been employed as standard drug carriers for the controlled adsorption and release of drug molecules in comparison to well-known OMS SBA-15 and MCM-41. The cytotoxicity analysis demonstrated that regular COK-12 particles were less harmful to mammalian cultured cells, causing lower apoptosis induction than modified COK-12, MCM-41, and SBA-15 particles.Thus, regular COK-12 was further used to prepare a dual antibiotic-loaded drug delivery material, followed by surface functionalization with Staphylococcus aureus-specific aptamers for targeting. The results demonstrated that the joint loading of lysozyme and vancomycin in regular COK-12 improved the ability of the antibiotic treatments to kill methicillin-resistant Staphylococcus strains via aptamer targeting. The minimum inhibitory concentration (MIC) values decreased 4.1-fold and 12-fold compared to the non-targeted use of the antimicrobial agents in homogeneous solutions for vancomycin and lysozyme, respectively, clearly demonstrating the high potential of COK-12 to be used as a carrier in multidrug therapy.
