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    Characterization of cancer stem cell properties and identification of invasion as well as metastatic process in head and neck cancer
    (Amer Assoc Cancer Research, 2015) Gunduz, Mehmet; Hatipoglu, Omer Faruk; Gunduz, Esra; Cetin, Elif Nihan; Uctepe, Eyyup; Cigdem, Sadik; Grenman, Reidar
    [Abstract Not Available]
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    Coffin-Siris syndrome with cafe-au-lait spots, obesity and hyperinsulinism caused by a mutation in the ARID1B gene
    (Int Research & Cooperation Assoc Bio & Socio-Sciences Advancement, 2016) Sonmez, Fatma Mujgan; Uctepe, Eyyup; Gunduz, Mehmet; Gormez, Zeliha; Erpolat, Seval; Oznur, Murat; Sagiroglu, Mahmut Samil
    Coffin-Siris syndrome (CSS) (MIM 135900) is characterized by developmental delay, severe speech impairment, distinctive facial features, hypertrichosis, aplasia or hypoplasia of the distal phalanx or nail of the fifth digit and agenesis of the corpus callosum. Recently, it was shown that mutations in the ARID1B gene are the main cause of CSS, accounting for 76% of identified mutations. Here, we report a 15 year-old female patient who was admitted to our clinic with seizures, speech problems, dysmorphic features, bilaterally big, large thumb, cafe-au-lait (CAL) spots, obesity and hyperinsulinism. First, the patient was thought to have an association of neurofibromatosis and Rubinstein Taybi syndrome. Because of the large size of the NF1 gene for neurofibromatosis and CREBBP gene for Rubinstein Taybi syndrome, whole exome sequence analysis (WES) was conducted and a novel ARID1B mutation was identified. The proband WES test identified a novel heterozygous frameshift mutation c.3394_3395insTA in exon 13 of ARID1B (NM_017519.2) predicting a premature stop codon p.(Tyr1132Leufs*67). Sanger sequencing confirmed the heterozygous c. 3394_3395insTA mutation in the proband and that it was not present in her parents indicating de novo mutation. Further investigation and new cases will help to understand this phenomenon better.
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    Designing an alternative reporter system for the GFP reporter system using Escherichia coli BL21 strain
    (Canadian Soc Clinical Investigation, 2015) Orhan, Ibrahim Y.; Karadag, Hizir A.; Bestepe, Furkan; Gul, Fatih; Uctepe, Eyyup; Yilmaz, Burak
    Purpose: Recombinant DNA technology can be used to transfer genetic material to bacteria [1]. To demonstrate that these recombinant bacteria can produce proteins by expressing the added genetic material, reporter systems are indispensable and mandatory [2,3]; hence, the improvement and development of reporter systems play a pivotal role in the progression of experimental method in recombinant DNA technology [2,4]. Methods: Viewing colour changes in the experimental area or on experiemntal subjects is simple, cheap and expedient [2, 5, 6]. In spite of their widespread utilization and the reliability of the consequence data, these reporter systems have some grave disadvantages [2,7,8]. In the absence of alternatives for these reporter systems, despite the serious handicaps and disadvantages, studies in recombinant DNA technology have been constricted by the infeasibility of such reporter systems [9,10]. Results: We focused on an alternative system to ameliorate current problems of common reporter systems - foremost the issue of time. The system in design had to be both potent and inexpensive. The main focus of the study was to design an alternative to the 2008 Nobel prize-winning GFP reporter system. Unlike the function of the GFP reporter system based on synthesizing colour absent in the medium as a means of response, we designed a system based on the degradation of dyes. Conclusion: This novel approach reduced the necessary time to attain a noticeable colour change and increased the certainty of the data.
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    Loss of heterozygosity in ING3 and ING5 genes in breast cancer
    (Tubitak Scientific & Technological Research Council Turkey, 2014) Gunduz, Esra; Nas, Gokhan; Acar, Muradiye; Uctepe, Eyyup; Bozer, Mikdat; Oznur, Murat; Bayrak, Reyhan
    The tumor suppressor genes (TSGs) ING3 and ING5, members of the inhibitor of growth gene family, are effective in inhibition of cell growth and induction of apoptosis. However, in many cancer types, one of the alleles of a TSG is lost through carcinogenesis, while the remaining allele is usually inactivated through a process called loss of heterozygosity (LOH). Previous studies in head and neck cancer revealed that allelic loss and reduced expression is a common pattern of ING gene family members. Fifty paraffin-embedded breast cancer tissues were analyzed by polymerase chain reaction and denatured-polyacrylamide gel electrophoresis for LOH status. The allelic deletion frequency of ING3 and ING5 were detected as 14% and 17% in breast cancer patients, respectively. No significant relationship was detected between ING3 LOH status and clinicopathological variables. Our data also suggest that both ING3 and ING5 LOH statuses have no significant effect in overall survival and disease-free survival of breast cancer patients. These results provide a rational explanation and relative contribution for the complexity of tumor formation, whereby allelic loss of ING3 and ING5 genes is not a major factor for breast cancer but is rather a part of a larger complex mechanism.
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    Matrix Metalloproteinases 2 and 9 Polymorphism in Patients With Myeloproliferative Diseases A STROBE-Compliant Observational Study
    (Lippincott Williams & Wilkins, 2015) Maral, Senem; Acar, Muradiye; Balcik, Ozlem Sahin; Uctepe, Eyyup; Hatipoglu, Omer Faruk; Akdeniz, Derya; Altun, Hatice Uludag
    Chronic myeloproliferative disorders such as polycythemia vera (PV), essential thrombocytosis (ET), and idiopathic myelofibrosis arise from clonal proliferation of neoplastic stem cells in the bone marrow. Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that have potential to degrade all types of extracellular matrix (ECM) and also play a role in remodeling of the ECM. It is known that MMPs play a role in bone marrow remodeling. The primary goal of our study is to explore the relationship between chronic myeloproliferative diseases and some of MMP gene polymorphisms. The demonstration of a relationship will help to understand whether these polymorphisms may be a potential early diagnosis marker of the diseases. Patients were selected from outpatient clinks of Turgut Ozal University Hospital, Ankara, Turkey, between December 2010 and May 2011. Twenty-eight patients that previously diagnosed and followed-up with PV, 17 with secondary polycythemia (SP), and 12 with ET were enrolled in the study, along with a control group of 22 healthy people. DNA was isolated from peripheral blood. Using polymerase chain reaction restriction fragment length polymorphism method, MMP2 and MMP9 gene polymorphisms were analyzed with agarose gel electrophoresis. There was a statistically significant difference between the study groups and the control group in terms of Gin279Arg polymoiphisms rates of MMP9. The highest MMP9 Gln279Arg polymorphism rate was observed in the ET group. But nobody from the control group had polymorphic MMP9. There was no statistically significant difference between the groups in terms of MMP2-735 C > T polymorphism rates. In conclusion, MMP9 gene Gln279Arg polymorphism was associated with ET, SP, and PV diseases. Hence, we believe that these gene polymorphisms may play a role in the mechanism of bone marrow fibrosis and may be a factor that increases the risk of thrombosis. Illumination of the molecular basis of the relationship between MMP-thrombosis and MMP-librosis provides a better understanding of the pathophysiology of PV and ET diseases mid will allow new approaches to diagnosis and treatment.