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    The emphasis of tumor suppressor genes and oncogenes in diagnosis and prognosis of anaplastic brain tumors [Anaplastik beyin tümörlerinin tani{dotless} ve prognozunda tümör süpressör genlerin ve onkogenlerin önemi]
    (2012) Avci Ç.B.; Susluer S.Y.; Dodurga Y.; Akalin T.; Cogulu O.; Dalbasti T.; Oktar N.; Gunduz C.
    The aim of the study is to the determine the profiles of tumor suppressor genes and oncogenes which cause brain tumor, establishing the association between the prognosis of cancer and the quantitation of genetic and epigenetic changes, and bringing a molecular approach to definite diagnosis. For this purpose, explant cell cultures are performed from the anaplastic brain tumor tissues of the cases. The expression analysis of the tumor suppressor genes (p53, RB1, PTEN, MGMT, RUNX3, DMBT1, PIKE) and oncogenes (EGFR, PIK3CA, MDM2, Olig2, GSTT1, COX-2 and hTERT) were determined by comparing the expression of GAPDH housekeeping gene using real-time online RT-PCR. The promoter regions of all the tumor suppressor genes' hypermethylation and also methylated and unmethylated copy numbers were determined with Q-PCR by using methylation specific primer and probes and the quantitation was carried out by comparing with each other. A significant difference was determined among the oncogenes; EGFR and hTERT gene expressions in patient tumor group. hTERT gene expression showed a significant difference with tumor grades. DMBT1 gene expression showed a significant difference with tumor grades. A prominent decrease was found in the aberration of tumor suppressor gene copy number in the glioma group. Gene copy number and gene expression of GSTT1 gene showed a significant correlation. RB1 and MGMT promoter methylation showed a significant difference in tumor patient group. Over expression of PIK3CA, EGFR and COX-2 among oncogenes and loss of copy number of PTEN, RB1 and RUNX3 among tumor suppressor genes found associated with short survival.
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    Experimental repair of rabbit segmental bone defects by using autologous bone marrow and electrical stimulation [Otolog kemik İligi ve elektriksel uyari{dotless} ile tavşan segmental kemik defektlerinin deneysel onari{dotless}mi{dotless}]
    (Turkiye Klinikleri, 2010) Gürbüz Y.; Şahin F.; Özdedeli S.; Öktem G.; Avci Ç.B.; Saydam, G..; Özdemir O.
    Objective: In this study, we have aimed to investigate the potential role of autologous bone marrow cell injection and muscular electrical stimulation as a separate and concomitant application on bone healing in experimental rabbit ulnar segmental bone defect model. Material and Methods: Forty New-Zealand rabbits, all over three months of age and weighing between 2500 and 3500 grams were divided into four groups. Four groups of rabbits were the control group (I), electrical stimulation group (II), bone marrow cells injection group (III) and bone marrow cells injection with electrical stimulation group (IV). Bone defect healing was evaluated radiologically according to the modified Lane and Sandhu scoring system and at the end of the sixth week, rabbits were sacrificed and their forearms were sampled for histopathological investigation. Results: When one-to-one comparison between all groups was performed, defect healing was found to be better in Groups II, III, and IV compared to Group I based on the radiological and histopathological parameters evaluated. This evaluation revealed that the healing was better in groups treated with bone marrow cell injection with or without electrical stimulation as well as in group treated with electrical stimulation compared to the control group with no treatment. Conclusion: Autologous bone marrow cells with or without electrical stimulation, would be used in healing of segmental bone defect with an adequate efficacy. Future stem cell studies combined with electrical current are required to demonstrate and to confirm that electrical current enhances in vivo cellular differentiation. © 2010 by Türkiye Klinikleri.
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    Hypericium perforatum extract ( St. John's Wort) and hypericin induce apoptosis in leukemic HL-60 cells by effecting h-TERT activity
    (2007) Özen K.P.; Şahin F.; Avci Ç.B.; Hişil Y.; Gündüz C.; Saydam, G..
    Hypericin is the main active component of Hypericium perforatum (St. John's Wort). Hypericin has been proven to have antitumoral effect in in vitro condition against solid tumors by deteriorating the mitochondrial functions. It has also anti-leukemic effect in in vitro conditions. However, there has not been any comparative study with hypericin and extract obtained from Hypericium perforatum L. In this study, it has been aimed to investigate the potential cytotoxic role of the extract obtained from Hypericium perforatum grown in Ege region on leukemic cell line, to compare the cytotoxic effects of both extract and hypericin in HL-60 cells, and to clarify the underlying mechanism(s) of this cytotoxicity. Hypericium perforatum extract was used in dilutions as 1/ 1000, 1/5000, 1/10.000, 1/50.000 and the IC50 value was found to be as 1/10.000 dilution. Hypericin was found to have cytotoxicity in HL-60 cells in time and dose dependent manner between the doses of 1nM to 100 µM with IC50 dose of 0.5 µM. Hypericin with the dose of 0.5 µM had similar cytotoxicity pattern with the cytotoxicity curve obtained with 1/ 10000 diluted extract. Apoptosis as an underlying mechanism of this cytoxocity was shown in HL-60 cells after incubation with IC50 dose of hypericin which was more remarkable at 48th hours by using acridine orange/ethidium bromide dye method. Total RNA was isolated concomittantly and h-TERT mRNA expression was analyzed at Light Cycler Real-time online polymerase chain reaction and it was found that the mRNA expression was meaningfully decreased at 48th hour of incubation of cells with hypericin. According to results of this study, we have shown that hypericin, as main cytotoxic compound of Hypericium perforatum L, induces apoptosis in HL-60 cells via effecting h-TERT mRNA expression. © Turkish Society of Hematology.
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    The roles of non-coding RNAs in Parkinson’s disease
    (Springer Netherlands, 2016) Majidinia M.; Mihanfar A.; Rahbarghazi R.; Nourazarian A.; Bagca B.G.; Avci Ç.B.
    Parkinson’s disease (PD) is considered as a high prevalence neurodegenerative disorders worldwide. Pathologically, the demise of dopamine-producing cells, in large part due to an abnormal accumulation of the ?-synuclein in the substantia nigra, is one of the main causes of the disease. Up until now, many de novo investigations have been conducted to disclose the mechanisms underlying in PD. Among them, impacts of non-coding RNAs (ncRNAs) on the pathogenesis and/or progression of PD need to be highlighted. microRNAs (miRNAs) and long ncRNAs (lncRNAs) are more noteworthy in this context. miRNAs are small ncRNAs (with 18–25 nucleotide in length) that control the expression of multiple genes at post-transcriptional level, while lncRNAs have longer size (over 200 nucleotides) and are involved in some key biological processes through various mechanisms. Involvement of miRNAs has been well documented in the development of PD, particularly gene expression. Hence, in this current review, we will discuss the impacts of miRNAs in regulation of the expression of PD-related genes and the role of lncRNAs in the pathogenesis of PD. © 2016, Springer Science+Business Media Dordrecht.