Browsing by Author "Tuna, Bilge Guvenc"
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Article Citation Count: 6Detection of viruses by probe-gated silica nanoparticles directly from swab samples(Elsevier, 2022) Dursun, Ali Doğan; Özalp, Veli Cengiz; Ercan, Meltem Kazak; Kavruk, Murat; Kavruk, Murat; Dursun, Ali Dogan; Ozalp, Veli Cengiz; Basic Sciences; Nutrition and DieteticsViral infection has been one of the major health issues for human life. The real-time reverse transcription polymerase chain reaction (RT-PCR)-based detection has primarily been used for virus detection as a highly reliable procedure. However, it is a relatively long and multi-stage process. In addition, required skilled personnel and complex instrumentation presents difficulties in large scale monitoring efforts. Therefore, we report here a direct and fast detection method for CoV-2 genome as applied in the nose-throat swab samples without any further processing. The detection principle is based on fluorescein-loaded mesoporous silica nanoparticles capped by specific gene sequences probes immobilized on the surface of the nanoparticles. Upon hybridization with the target viral genome, the fluorescein molecules were released from the mesopores. Testing with synthetic oligonucleotides, the NSP12 gene-based detection resulted in a strong signal. Target detection time could be optimized to 15 min and the limit of detection was 1.4 RFU with 84% sensitivity with clinical samples (n = 43).Article Citation Count: 0Direct Detection of Viral Infections from Swab Samples by Probe-Gated Silica Nanoparticle-Based Lateral Flow Assay(Wiley-v C H verlag Gmbh, 2024) Özalp, Veli Cengiz; Dogan, Soner; Tekol, Serap Demir; Celik, Caner; Ozalp, Veli Cengiz; Tuna, Bilge Guvenc; Basic SciencesPoint-of-care diagnosis is crucial to control the spreading of viral infections. Here, universal-modifiable probe-gated silica nanoparticles (SNPs) based lateral flow assay (LFA) is developed in the interest of the rapid and early detection of viral infections. The most superior advantage of the rapid assay is its utility in detecting various sides of the virus directly from the human swab samples and its adaptability to detect various types of viruses. For this purpose, a high concentration of fluorescein and rhodamine B as a reporting material was loaded into SNPs with excellent loading capacity and measured using standard curve, 4.19 mu mol & sdot; g-1 and 1.23 mu mol & sdot; g-1, respectively. As a model organism, severe acute respiratory syndrome coronavirus-2 (CoV-2) infections were selected by targeting its nonstructural (NSP9, NSP12) and envelope (E) genes as target sites of the virus. We showed that NSP12-gated SNPs-based LFA significantly outperformed detection of viral infection in 15 minutes from 0.73 pg & sdot; mL-1 synthetic viral solution and with a dilution of 1 : 103 of unprocessed human samples with an increasing test line intensity compared to steady state (n=12). Compared to the RT-qPCR method, the sensitivity, specificity, and accuracy of NSP12-gated SNPs were calculated as 100 %, 83 %, and 92 %, respectively. Finally, this modifiable nanoparticle system is a high-performance sensing technique that could take advantage of upcoming point-of-care testing markets for viral infection detections. Here, universal-modifiable probe-gated silica nanoparticles (SNPs) based lateral flow assay (LFA) is developed in the interest of the rapid and early detection of viral infections. The most superior advantage of the rapid assay is its utility in detecting various sides of the virus directly from the human swab samples and its adaptability to detect various types of viruses. The NSP12, NSP9, and E gene targets of CoV-2 were used as detection targets.imageArticle Citation Count: 0Identification of Bacterial Vaginal Microbiota via Metagenomic Approach(Galenos Publ House, 2022) Özalp, Veli Cengiz; Sudagidan, Mert; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Tuna, Bilge Guvenc; Ozalp, Veli Cengiz; Basic SciencesAim: 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.Article Citation Count: 0Long-term intermittent caloric restriction remodels the gut microbiota in mice genetically prone to breast cancer(Elsevier Science inc, 2024) Balcı, Tuğçe Nur; Çetiner, Özlem; Dogan, Aysenur; Sudagidan, Mert; Balci, Tugce Nur; Cetiner, Ozlem; Tuna, Bilge Guvenc; Nutrition and DieteticsObjectives: Gut microbiota dysbiosis is among the risk factors for breast cancer development, together with genetic background and dietary habits. However, caloric restriction has been shown to remodel the gut microbiota and slow tumor growth. Here, we investigated whether the gut microbiota mediates the preventive effects of long-term chronic or intermittent caloric restriction on breast cancer predisposition. Methods: 10-week-old transgenic breast cancer-prone mice were randomly assigned to dietary groups (ad libitum, chronic caloric restriction, and intermittent caloric restriction groups) and fed up to week 81. Stool samples were collected at weeks 10 (baseline), 17 (young), 49 (adult), and 81 (old). 16S rRNA gene sequencing was performed to identify the gut microbiota profile of the different groups. In order to investigate the breast cancer gut microbiota profile within genetically predisposed individuals regardless of diet, mammary tumor-bearing mice and mammary tumor-free but genetically prone mice were selected from the ad libitum group (n = 6). Results: Intermittent caloric restriction increased the microbial diversity of adult mice and modified age- related compositional changes. A total of 13 genera were differentially abundant over time. Pathogenic Mycoplasma was enriched in the re-feeding period of the old intermittent caloric restriction group compared with baseline. Furthermore, mammary tumor-free mice showed shared gut microbiota characteristics with mammary tumor-bearing mice, suggesting an early link between genetic predisposition, gut microbiota, and breast cancer development. Conclusions: Our study revealed the role of gut microbes in the preventive effects of caloric restriction against breast cancer development, implying the significance of diet and microbiome interplay. (c) 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.