Browsing by Author "Ucak, Samet"

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Citation - WoS: 13
Citation - Scopus: 17
Determination of Bacterial Community Structure of Turkish Kefir Beverages Via Metagenomic Approach
(Elsevier Sci Ltd, 2022) Yegin, Zeynep; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Altunbas, Osman; Ucak, Samet; Sudagidan, Mert; 01. Atılım University
Bacterial microbiota of industrially produced kefir beverages (n:33) consumed in Turkey was studied using a culture-independent method and a metagenomic approach. DNA extraction from non pre enriched and pre-enriched kefir samples was used for 16S rRNA amplicon sequencing. Kefirs were dominated by Firmicutes, followed by Actinobacteria and Proteobacteria phyla. The most abundant genera in non pre-enriched kefir beverages were Lactococcus followed by Streptococcus, Bifidobacterium, Lactobacillus, and Leuconostoc. Pre-enriched kefirs were dominated by Streptococcus followed by Lactobacillus, Lactococcus, Bifidobacterium, and Leuconostoc at the genus level. Psychroserpens, Desulfonispora, Pediococcus, Micromonospora, Fructobacillus, Mycobacterium, Acetobacter, Pseudopedobacter, and Clostridium XI genera were found only in pre-enriched kefirs. Kefirs displayed pH differences from 4.04 to 4.49 and the acidity was 0.617e0.987. In two samples, the lowest pH values were obtained with abundance of Lactobacillus helveticus and Streptococcus salivarius. This study broadens our viewpoint and strengthens future applications of kefir beverages in industrial and medical fields. (C)& nbsp;2022 Elsevier Ltd. All rights reserved.
Enhancement of Paclitaxel Therapeutic Effect by Aptamer Targeted Delivery in Plga Nanoparticles
(2021) Dursun, Ali; Dursun, Ali Doğan; Ucak, Samet; Özalp, Veli Cengiz; Poyraz, Fatma Sayan; Yilmaz, Elif; Mansuroglu, Banu; Ozalp, Veli Cengiz; Dursun, Ali Doğan; Özalp, Veli Cengiz; Basic Sciences; Basic Sciences; 08. Medical School; 01. Atılım University
Objectives: Paclitaxel is a drug molecule used in the therapy of various cancer types, including breast cancer. It is one of the preferred chemotherapy agent due to its high efficacy. However, many side effects have been observed associ- ated with paclitaxel use such as allergy, hair loss, diarrhea and pain. Methods: We evaluated therapeutic efficacy of paclitaxel when it is actively targeted to breast cancer tumours inside a polymeric nanoparticle. Targeted delivery of paclitaxel to tumour sites has been reported as an improved cytotoxicity strategy with a variety of nanoparticles. In this study, poly Lactic-co-Glycolic Acid (PLGA) nanoparticles were used as drug carrier and nucleolin aptamers as affinity targeting agents. Results: Paclitaxel molecules were entrapped during the synthesis of PLGA nanoparticles of 238 nm in diameter. The encapsulation and loading efficiencies of paclitaxel was 97% and 21% respectively. The paclitaxel loaded PLGA nanoparticles were functionalized with nucleolin aptamers and their targeting ability to cultured mouse cancer cells was determined for two cell lines (E0771 and 4T1). E0771 cell line was chosen for the preparation of allograph breast cancer mouse models. Evaluations of the targeted paclitaxel in PLGA nanoparticles showed 38% better performance in inhibiting tumour growth compared to free paclitaxel treatment groups of mouse models. Conclusion: The chemotherapeutic effect of cancer drugs like paclitaxel can be increased by loading inside tumour targeted polymeric nanoparticles
Citation - WoS: 22
Citation - Scopus: 25
Identification 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, Mert; 01. Atılım University
Bacterial 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.
Identification of Bacterial Vaginal Microbiota Via Metagenomic Approach
(Galenos Publ House, 2022) Ucak, Samet; Sudagidan, Mert; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Tuna, Bilge Guvenc; Ozalp, Veli Cengiz; Basic Sciences; 08. Medical School; 01. Atılım University
Aim: The aim of the current study was to identify vaginal bacterial microbiota of 38 Turkish women using the high -throughput next -generation sequencing and metagenomic approach at different taxonomic levels from the kingdom to the species level. Materials and Methods: Vaginal swab samples (n=38) were collected in the DNA/RNA shield collection tubes at Yeditepe University Hospital, Department of Obstetrics and Gynecology in June 2021 and DNA extraction was performed by ZymoBIOMICS DNA miniprep kit. The information related to age, marital status, preliminary diagnosis and anamnesis status of patients were collected. To determine the vaginal microbiota, a metagenomic approach was applied using 16S rRNA amplicon sequencing. Results: The dominant phylum Firmicutes was followed by Proteobacteria, Actinobacteria, Tenericutes, Fusobacteria, and Synergistetes in the vaginal samples. Lactobacillus was the most abundant genus followed by Prevotella, Enterobacter, Gardnerella, and Dialister. Lactobacillus iners was dominant at the species level in vaginal swab samples, followed by Gardnerella vaginalis, Enterobacter tabaci, Prevotella timonensis, Prevotella bivia, and Lactobacillus jensenii. Canonical correspondence analysis (CCA) showed that Proteobacteria and Fusobacteria were mainly related to married/single variable with the highest percentages, whereas Actinobacteria and Tenericutes were related to age variable at the phylum level. Campylobacter , Atopobium , Enterobacter , and Lactococcus were mainly found in married/single variable with the highest percentages, whereas Anaerococcus, Streptococcus, Sutterella , and Veillonella were related to age. Moreover, CCA showed that Campylobacter ureolyticus, Lb. jensenii , and Atopobium vaginae were associated with married/single variable, whereas Lactobacillus johnsonii and G. vaginalis were found in age variable with the highest percentages at the species level. Conclusion: Vaginal diseases are still a major public health concern. The vaginal microbiota, which has been studied in more depth in recent years, has been discovered to be more complicated than previously imagined thanks to technological developments. More patient investigations are needed to confirm and develop these findings.
Citation - WoS: 38
Citation - Scopus: 46
Inhibitory Effects of Aptamer Targeted Teicoplanin Encapsulated Plga Nanoparticles for staphylococcus Aureus Strains
(Springer, 2020) Ucak, Samet; Özalp, Veli Cengiz; Sudagidan, Mert; Borsa, Baris A.; Mansuroglu, Banu; Ozalp, Veli C.; Özalp, Veli Cengiz; Basic Sciences; Basic Sciences; 08. Medical School; 01. Atılım University
Emergence of resistance to traditional antibiotic treatments necessitates alternative delivery systems. Teicoplanin is a glycopeptide antibiotic used in the treatments of serious infections caused by Gram-positive bacteria, including Methicillin Resistant Staphylococcus aureus (MRSA). One strategy to keep up with antibiotic resistance development is to limit dose and amount during treatments. Targeted delivery systems of antibiotics have been suggested as a mechanism to slow-down the evolution of resistance and to increase efficiency of the antimicrobials on already resistant pathogens. In this study, we report teicoplanin delivery nanoparticles of Poly Lactic-co-Glycolic Acid (PLGA), which are functionalized with S. aureus specific aptamers. A 32-fold decrease in minimum inhibitory concentration (MIC) values of teicoplanin for S. aureus was demonstrated for susceptible strains and about 64-fold decline in MIC value was achieved for moderately resistant clinical isolates of MRSA upon teicoplanin treatment with aptamer-PLGA nanoparticles. Although teicoplanin delivery in PLGA nanoparticles without targeting demonstrated eightfold decrease in MIC of susceptible strains of S. aureus and S. epidermidis and twofold in MIC of resistant strains, the aptamer targeting specifically decreased MIC for S. aureus, but not for S. epidermidis. Therefore, aptamer-targeted PLGA delivery of antibiotic can be an attractive alternative to combat with some of the multi-drug resistant bacterial pathogens.
Citation - WoS: 2
Citation - Scopus: 2
A Metagenomic Survey of Bacterial Communities From Kurut: the Fermented Cow Milk in Kyrgyzstan
(Wiley-v C H verlag Gmbh, 2024) Yegin, Zeynep; Mamatova, Zhanylbubu; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Ucak, Samet; Sudagidan, Mert; 01. Atılım University
Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties. image
Citation - WoS: 23
Citation - Scopus: 20
Real-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.; Nutrition and Dietetics; Basic Sciences; 07. School of Health Sciences; 08. Medical School; 01. Atılım University
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.
Citation - WoS: 3
Citation - Scopus: 2
Targeted 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, Aleksander; Basic Sciences; 08. Medical School; 01. Atılım University
Different 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.