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Author: Ucak, SametCOAR Access Rights: open access

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    Article
    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
    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
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    Article
    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
    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.
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    Article
    Citation - WoS: 23
    Citation - Scopus: 26
    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
    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.