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    Biomarkers to target and silence stemness of breast cancer stem cell model: silencing MDR1 by siRNA
    (Walter De Gruyter Gmbh, 2022) Yildirim, Gamze; Kars, Meltem D.; Kars, Gokhan; Kilic, Hamdi S.
    Objectives Aim of the study was to reveal new biomarker genes to target breast cancer stem-like cells (BCSC-like) and then sensitize BCSC-like cells to chemotherapy by silencing MDR1 gene found to be the most suitable target. Methods Drug resistance associated genes were screened by cDNA microarray to unveil biomarker genes in drug resistance breast cancer model cells. Drug resistance was then reversed by silencing MDR1 gene in BCSC-like cells. The effect of silencing was monitored by real-time cell proliferation analysis. Differential expressions of MDR1, ALDH1A3, EGFR and BAG4 genes were identified by real-time PCR. P-glycoprotein (P-gp) expression level and its activity were investigated by Western blot and flow cytometry measurements, respectively. Results 16 new biomarker genes were identified upon gene expression analysis by cDNA microarray. MDR1 gene was selected as the most potent target gene and silencing of it caused down-regulation of MDR1, ALDH1A3, EGFR, BAG4 expression and P-glycoprotein activity and expression in BCSC-like cells. At the end, silenced BCSC-like cells were found to be more responsive to paclitaxel therapy. Conclusions In conclusion, siMDR1 silencing is an effective way to reverse multidrug resistance and malignancy. New biomarker genes revealed in this study require to be investigated to target stemness of BC.
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    Biomarkers to target and silence stemness of breast cancer stem cell model: silencing MDR1 by siRNA
    (Walter De Gruyter Gmbh, 2022) Yildirim, Gamze; Kars, Meltem D.; Kars, Gokhan; Kilic, Hamdi S.
    Objectives Aim of the study was to reveal new biomarker genes to target breast cancer stem-like cells (BCSC-like) and then sensitize BCSC-like cells to chemotherapy by silencing MDR1 gene found to be the most suitable target. Methods Drug resistance associated genes were screened by cDNA microarray to unveil biomarker genes in drug resistance breast cancer model cells. Drug resistance was then reversed by silencing MDR1 gene in BCSC-like cells. The effect of silencing was monitored by real-time cell proliferation analysis. Differential expressions of MDR1, ALDH1A3, EGFR and BAG4 genes were identified by real-time PCR. P-glycoprotein (P-gp) expression level and its activity were investigated by Western blot and flow cytometry measurements, respectively. Results 16 new biomarker genes were identified upon gene expression analysis by cDNA microarray. MDR1 gene was selected as the most potent target gene and silencing of it caused down-regulation of MDR1, ALDH1A3, EGFR, BAG4 expression and P-glycoprotein activity and expression in BCSC-like cells. At the end, silenced BCSC-like cells were found to be more responsive to paclitaxel therapy. Conclusions In conclusion, siMDR1 silencing is an effective way to reverse multidrug resistance and malignancy. New biomarker genes revealed in this study require to be investigated to target stemness of BC.
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    Hydrogen and poly-?-hydroxybutyric acid production at various acetate concentrations using Rhodobacter capsulatus DSM 1710
    (Pergamon-Elsevier Science Ltd, 2019) Demiriz, Burcu Ozsoy; Kars, Gokhan; Yucel, Meral; Eroglu, Inci; Gunduz, Ufuk
    In the present study, Rhodobacter capsulatus DSM 1710 was cultured in media having various concentrations of acetate (10-65 mM) to investigate simultaneous production of hydrogen and PHB. The highest cumulative hydrogen productions were observed using 50 mM (11.7 mmol H-2) and 65 mM (11.4 mmol H-2) acetate. However, molar productivity values were higher at 25 mM (0.50 mmol/Lc.h) and 50 mM (0.44 mmol/Lc.h) compared to 65 mM (0.35 mmol/Lc.h). Furthermore, the highest PHB production (234.7 mg/L) was attained using 65 mM acetate. At molecular level, the expressions of nifD and phaC genes were analyzed by reverse transcription-polymerase chain reaction using specifically designed tagged primers. Increasing acetate concentrations resulted in an increase in nifD and phaC expressions. Accordingly, the highest transcription levels were obtained at 65 mM acetate. The kinetic studies on hydrogen production and acetate consumption showed that hydrogen production data was in agreement with the Modified Gompertz Model and acetate was consumed through first order kinetics. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.
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    Unraveling the impact of primary immunodeficiency disorders on the microbiota of dental caries in children through 16S rRNA gene-based metagenomic analysis
    (Tubitak Scientific & Technological Research Council Turkey, 2023) Al-Kebsi, Bushra Lutf Ahmed; Kars, Gokhan; Ozer, Hazal; Guner, Sukru Nail
    Background/aim: Dental caries is a frequently occurring and multifactorial chronic disease in children resulting from the interaction of cariogenic bacteria and host susceptibility. The aim of this study was to elucidate the impacts of primary immunodeficiency disorders (PIDs) on microbiota of dental caries in children by 16S rRNA gene-based metagenomic analysis.Materials and methods: Enrolled in this study were 15 children with primary PID with caries (PID group) and 15 healthy children with caries as a control (CG). The DMFT index, saliva flow rate, and buffering capacity of each participant were assessed before the metagenomic analyses were conducted. For taxonomic profiling, the reads were obtained by high-throughput sequencing of the V3-V4 hypervariable region of 16S rRNA.Results: The DMFT score, saliva flow rate, and buffering capacity of the groups were similar. The flow rate and buffering capacity had no correlation with the number of species with 95% confidence. The metagenomic analysis resulted in the identification of 2440 bacterial species in all of the samples. Among the 50 most prevalent species present at >= 1% relative abundance, Prevotella melaninogenica and Prevotella salivae were differentially more abundant in the PID group. The PID group and CG showed similar species richness and evenness, but 4 of the 5 samples with the highest Shannon-Weiner and Inverse Simpson indices belonged to the PID group. The Spearman test results for correlation of the species in the PID subgroups showed that Prevotella oris had a positively correlated relationship with both Scardovia wiggsiae and Saccharibacteria genera incertae sedis.Conclusion: This study provided insight into the caries microbiota of children with immunodeficiency diseases. Differentially abundant species, novel bacterial associations, and unique bacterial species were disclosed in the PID samples, indicating the role of the immune system in altering the caries microbiota. The prominent bacterial species and associations in the PID group should be suspected in regard to their link with present or future diseases.