Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14627/7
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Article Comprehensive Proteomic and Metabolomic Analysis of Novel Substituted Fluoroquinolone Derivatives in Escherichia Coli Isolates(John Wiley and Sons Ltd, 2026) Nigiz Ş.; Kulabaş N.; Türe A.; Kablan S.; Koçak E.; Özkul C.; Küçükgüzel İ.; Koçak, Engin; Nigiz, Şeyma; Kablan, Sevilay Erdoğan; Özkul, Ceren; Kulabaş, Necla; Küçükgüzel, İlkay; Türe, AslıAntimicrobial resistance is one of the most important global problems, and new antibiotic requirements have been emerging as a key point in this issue. In the present work, we focused on the efficiency of two novel promising fluoroquinolone derivatives on resistant Escherichia coli isolates at the molecular level. Their mode of action and adaptation process were evaluated by using proteomics and metabolomics analysis. Proteomics analysis showed that two compounds have an effect mainly on the ribosomal process and energy metabolism. Moreover, we observed compounds that affect various important antimicrobial targets, such as ribosomal subunits, phosphotransacetylase, and chaperone proteins. In metabolomics analysis, we found that compounds altered bacterial metabolism directly. Pathway analysis showed that cofactor biosynthesis and energy metabolism were affected mainly by undertreated groups. Our experiments demonstrated that novel fluoroquinolone derivatives have promising results at the molecular level and results will contribute to further studies. © 2026 John Wiley & Sons Ltd.Article Fully Synthetic, Nature-Inspired Exosome-Mimetics for Melanoma Therapy(Elsevier B.V., 2026) Arda Ozturk N.Z.; Majchrzak O.B.; Ulivi G.; Kirmizibayrak P.B.; Borchard G.; Patrulea V.; Ozer O.; Ozturk, Nahide Zeren Arda; Borchard, Gerrit; Ozer, Ozgen; Patrulea, Viorica; Majchrzak, Oliwia Barbara; Arda Ozturk, Nahide Zeren; Kirmizibayrak, Petek Ballar; Ulivi, GianlucaFully synthetic exosome-mimetics (FSEMs) represent a nature-inspired drug delivery system designed to replicate the key physicochemical and biological properties of natural exosomes, while offering the potential to address limitations in scalability and reproducibility associated with natural exosomes. In this study, we prepared FSEMs at the laboratory scale. We loaded them with (–)-epigallocatechin-3-gallate (EGCG) and microRNA-23a (miR-23a), aiming to co-deliver therapeutic small molecules and nucleic acids for the treatment of melanoma. FSEMs were fabricated using three methods: thin-film hydration, ethanol injection, and microfluidics. They were surface-functionalized with either CD9, a tetraspanin involved in membrane fusion, or TSP-1, an adhesion protein promoting cellular interactions. Through physicochemical characterization via dynamic light scattering, we found that FSEMs were ∼ 100 nm in size, of low polydispersity (∼0.2) and showed a negative zeta potential (∼–55 mV). Both EGCG and miR-23a were efficiently encapsulated. SDS-PAGE analysis confirmed successful protein incorporation and correct positioning. In vitro release studies showed minimal premature leakage, supporting their suitability for cellular uptake-mediated delivery. When tested on melanoma cells (MDA-MB-435) and progenitor human dermal fibroblasts (FE002-SK2), FSEMs selectively killed melanoma cells while sparing fibroblasts. Importantly, EGCG within FSEMs was more effective than the free compound. Compared to conventional DOTAP-based liposomes, FSEMs were more selective and induced less off-target cytotoxicity. This study presents a proof-of-concept for fully synthetic, protein-functionalized FSEMs as dual carriers for both chemical and gene-based agents, offering a safer and potentially more effective alternative to traditional cationic liposomes. These results lay the groundwork for future in vivo validation and translational cancer research. © 2026 The Author(s)Article Investigation of the Susceptibility Rates to Ceftazidime-Avibactam and Colistin, Clonal Relationships, and Clinical Data of Patients with Carbapenem-Resistant Klebsiella Pneumoniae Isolates Detected in the ICUs of a Hospital in İstanbul(K Faisal Special Hospital Research Centre, 2026) Akkaya, Yuksel; Aydin, Irfan; Harmankaya, Sebile; Karakul, Mehmet; Aydin, Mehtap; Erdin, Begum Nalca; Kilic, Ibrahim Halil; Karakuş, MehmetBACKGROUND: The increase in carbapenem-resistant K. pneumoniae (CR-Kp) in intensive care units (ICUs) causes treatment difficulties and increases risk in mortality. OBJECTIVES: The aim of this study was to investigate the susceptibility rates of CR-Kp isolates obtained from ICUs to ceftazidime-avibactam (CAZ-AVI) and colistin, carbapenem resistance genes, clonal relationships and clinical characteristics of the patients. DESIGN: Retrospective cohort SETTING: Single-center, University of Health Sciences, & Uuml;mraniye Training and Research Hospital MATERIALS AND METHODS: This study was conducted between June 2023 and December 2024. Isolates were identified using VITEK MS v.3.2, and antibiotic susceptibility testing was performed using the VITEK 2 Compact system. CAZ-AVI susceptibility was determined using disk diffusion, and colistin susceptibility was determined using broth microdilution to determine minimum inhibitory concentration (MIC) values. Carbapenem resistance genes were determined using multiplex real-time polymerase chain reaction (RT-PCR) and clonal relationship arbitrarily primed-polymerase chain reaction (AP-PCR). MAIN OUTCOME MEASURES: Resistance genes of CR-Kp isolates, clonal relationships, CAZ-AVI and colistin resistance, and clinical characteristics of patients SAMPLE SIZE: Ninety-seven isolates from 76 patients RESULTS: Among patients with CR-Kp isolates, central venous catheter use was detected in 59 cases (78%), ventilator-associated pneumonia in 44 cases (58%), and bacteremia in 39 cases (51%), respectively. It was determined that 53 of the patients (70%) died. Using the AP-PCR method, 60 different genotypes were identified among 97 isolates, and clustering was determined in 42 of the isolates (46%). It was determined that 36 (37%) of the isolates were resistant to colistin and 42 (45%) were resistant to CAZ-AVI. NDM+OXA-48, OXA-48, KPC, KPC+NDM, and NDM genes were detected in 40 (43%), 32 (35%), 10 (11%), 2 (2%), and 3 (3%) isolates, respectively. It was determined that 30 (75%) of the isolates with NDM+OXA-48 and only 4 (12%) of the isolates with OXA-48 were resistant to CAZ-AVI. CONCLUSION: In addition to OXA-48, an increase in the frequency of CR-Kp isolates containing the NDM, NDM+OXA-48, KPC+NDM, and OXA-48+KPC genes were also detected. It was also determined that resistance to colistin and CAZ-AVI is increasing. The AP-PCR method can also be used to investigate infections. LIMITATIONS: Single center,Pulsed Field Gel Electrophoresis (PFGE) could not be performed together with AP-PCRArticle Machine Learning Model for Predicting Multidrug Resistance in Clinical Escherichia Coli Isolates: A Retrospective General Surgery Study(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Tolan, H.K.; Aydın, İ.; Tanyildizi-Kökkülünk, H.; Karakuş, M.; Akkaya, Y.; Kaya, O.; Işman, F.K.Background/Objectives: Escherichia coli is one of the leading causes of surgical site infections (SSIs) and poses a growing public health concern due to its increasing antimicrobial resistance. High rates of extended-spectrum beta-lactamase (ESBL) production among E. coli strains complicate treatment outcomes and emphasize the need for effective surveillance and control strategies. Methods: A total of 691 E. coli isolates from general surgery clinics (2020–2025) were identified using MALDI-TOF MS. Antibiotic susceptibility data and patient variables were cleaned, encoded, and used to predict resistance using the Random Forest, CatBoost, and Naive Bayes algorithms. SMOTE addressed class imbalance, and model performance was assessed through various validation methods. Results: Among the three machine learning models tested, Random Forest (RF) showed the best performance in predicting antibiotic resistance of E. coli, achieving median accuracy, precision, recall, and F1-scores of 0.90 and AUC values up to 0.99 for key antibiotics. CatBoost performed similarly but was less stable with imbalanced data, while Naive Bayes showed lower accuracy. Feature importance analysis highlighted strong inter-antibiotic resistance links, especially among β-lactams, and some influence of demographic factors. Conclusions: This study highlights the potential of simple, high-performing models using structured clinical data to predict antimicrobial resistance, especially in resource-limited clinical settings. By incorporating machine learning into antimicrobial resistance (AMR) surveillance systems, our goal is to support the advancement of rapid diagnostics and targeted antimicrobial stewardship approaches, which are essential in addressing the growing challenge of multidrug resistance. © 2025 by the authors.Article Citation - WoS: 5Citation - Scopus: 5Effects of <i>myrtus Communis</I> L. Extract and Apocynin on Lens Oxidative Damage and Boron Levels in Rats With a High Fat-Diet(Galenos Publ House, 2021) Yasar, Ruya Kuru; Kuru, Dilruba; Sen, Ali; Sener, Goksel; Ercan, Feriha; Yarat, Aysen; Kuru, RuyaObjectives: Nutritional obesity causes oxidant damage in the body and cataract formation in the lenses by increasing the formation of free radicals. Myrtus communis leaf extracts (Myr) have antioxidant properties, and apocynin (Apo) is an effective NADPH-oxidase inhibitor. The data on tissue boron levels are quite lacking. The aim of this novel study was to investigate the effects of Myr and Apo treatment on boron levels and oxidative lens damage in rats fed a high-fat diet (HFD). Materials and Methods: Wistar albino male rats were randomly divided into four groups: the control group, HFD group, HFD + Myr group, and HFD + Apo group. Body weight and blood lipids were determined before and after the experiment. After decapitating the rats, the lenses were removed and homogenized. Catalase (CAT) and superoxide dismutase (SOD) activities and boron, malondialdehyde (MDA), and reduced glutathione (GSH) levels in the lens homogenates were determined. Results: The HFD increased serum triglyceride (p<0.05), total cholesterol level (p<0.001), body weight (p<0.001), and lens MDA levels (p<0.01) and decreased lens GSH (p<0.05) and boron level (p<0.01), SOD (p<0.001), and CAT activity (p<0.001). However, Myr and Apo treatment reduced the rats' body weight (p<0.001), serum triglyceride (p<0.05), and total cholesterol level (p<0.001) and increased lens boron (p<0.01; p<0.001), GSH levels (p<0.05; p<0.01), and CAT activity (p<0.001). Conclusion: Both Myr and Apo may be able to reduce oxidative stress in the lenses of obese rats caused by HFD by increasing boron levels.