Researcher:
Babuççu, Gizem

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Master Student

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Gizem

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Babuççu

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Babuççu, Gizem

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20212

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    PublicationOpen Access
    Comparison of crystal violet staining assay and XTT methods in the evaluation of biofilm formation in Candida parapsilosis candidemia isolates
    (Design Oriented Community (DOC), 2021) Can, Füsun; Doğan, Özlem; Ataç, Nazlı; Babuççu, Gizem; Faculty Member; Faculty Member; Researcher; School of Medicine; Graduate School of Health Sciences; 103165; 170418; N/A; N/A
    Objective: biofilm formation is one of the most important virulence factors of Candida species which leads to permanent infection foci by adhering to foreign materials and which are difficult to treat. Candida parapsilosis, which is one of the most common causes of candidemia in our country, is frequently isolated as a causative agent in catheterrelated infections. The most commonly used methods for evaluating the biofilm formation of Candida species are measuring cell viability with XTT (2,3-bis (2-methoxy-4-nitro-5- sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide) and evaluating the total biofilm mass with crystal violet (CV). The aim of this study is to evaluate the biofilm formation ability of C. parapsilosis candidemia isolates by XTT and (CV) methods and compare these methods with each other. Materials and methods: C. parapsilosis isolates sent from various hospitals between 2015 and 2019 were included in the study retrospectively, and the species-level identification was performed using the matrix- assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) The biofilm formation of the isolates was compared based on the optical density (OD) values obtained by crystal violet and XTT methods. The biofilm formation of the isolates was evaluated by categorizing them into low, medium and high biofilm groups as ± 20% according to the median value of all strains. Results: totally, 79 C. parapsilosis candidemia isolates were included in this study and categorical compatibility between CV and XTT methods in low, medium and high biofilm groups was found as 69.6%, 60.6% and 73.9%, respectively. The OD values of the XTT method in the high biofilm group were found statistically significantly higher when compared with the values from the CV method. Conclusion: the compatibility of XTT and crystal violet methods in terms of biofilm measurement in C. parapsilosis isolates was considered acceptable, and no major variations were detected between the categories. According to these results, when evaluating the biofilm levels of C. parapsilosis isolates, high OD values obtained by the XTT method should be confirmed with the CV method.
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    PublicationOpen Access
    Existence of SARS-Cov-2 RNA on ambient particulate matter samples: a nationwide study in Turkey
    (Elsevier, 2021) Arı, Akif; Şahin, A. Ülkü; Gaga, O. Eftade; Kuzu, S. Levent; Arı Ertürk, Pelin; Odabaşı, Mustafa; Taşdemir, Yücel; Cindoruk, S. Sıddık; Esen, Fatma; Çalışkan, Burak; Sakin, Egemen; Tecer, H. Lokman; Fıçıcı, Merve; Altın, Ahmet; Onat, Burcu; Ayvaz, Coşkun; Uzun, Burcu; Saral, Arslan; Döğeroğlu, Tuncay; Malkoç, Semra; Üzmez, Ö. Özlem; Kunt, Fatma; Aydın, Senar; Kara, Melik; Yaman, Barış; Doğan, Güray; Olgun, Bihter; Dokumacı, N. Ebru; Güllü, Gülen; Uzunpınar, S. Elif; Kayalar, Özgecan; Konyalılar, Nur; Doğan, Özlem; Can, Füsun; Babuççu, Gizem; Bayram, Hasan; Researcher; PhD Student; Faculty Member; Faculty Member; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); School of Medicine; Graduate School of Health Sciences; N/A; N/A; 170418; 103165; N/A; 4890
    Coronavirus disease 2019 (COVID-19) is caused by the SARS-CoV-2 virus and has been affecting the world since the end of 2019. The disease led to significant mortality and morbidity in Turkey, since the first case was reported on March 11th, 2020. Studies suggest a positive association between air pollution and SARS-CoV-2 infection. The aim of the present study was to investigate the role of ambient particulate matters (PM), as potential carriers for SARS-CoV-2. Ambient PM samples in various size ranges were collected from 13 sites including urban and urban-background locations and hospital gardens in 10 cities across Turkey between 13th of May and 14th of June 2020 to investigate the possible presence of SARS-CoV-2 RNA on ambient PM. A total of 203 daily samples (TSP, n = 80; PM2.5, n = 33; PM2.5-10, n = 23; PM10?m, n = 19; and 6 size segregated PM, n = 48) were collected using various samplers. The N1 gene and RdRP gene expressions were analyzed for the presence of SARS-CoV-2, as suggested by the Centers for Disease Control and Prevention (CDC). According to real time (RT)-PCR and three-dimensional (3D) digital (d) PCR analysis, dual RdRP and N1 gene positivity were detected in 20 (9.8%) samples. Ambient PM-bound SARS-CoV-2 was analyzed quantitatively and the air concentrations of the virus ranged from 0.1 copies/m3 to 23 copies/m3. The highest percentages of virus detection on PM samples were from hospital gardens in Tekirdağ, Zonguldak, and Istanbul, especially in PM2.5 mode. Findings of this study have suggested that SARS-CoV-2 may be transported by ambient particles, especially at sites close to the infection hot-spots. However, whether this has an impact on the spread of the virus infection remains to be determined.