Browsing by Author "Atalay, Arzu"
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Item Analysis of global microRNAome profiles of Caenorhabditis elegans oocytes and early embryos(2016) Atalay, Arzu; Biyoteknoloji Enstitüsü; Güçlü Durgun, SelenOne of the most complex cell transformations in biology is the remodeling of a fertilized oocyte into a totipotent zygote. There is no transcription during this event, and therefore mRNAs and proteins accumulated in the oocyte during oogenesis are utilized until zygotic genome activation. In order to differentiate into somatic cells, the embryo must erase the totipotency signature coming from the oocyte cytoplasm in the somatic blastomeres. In this study, the microRNAome profiles of oocytes and early embryos before and after zygotic genome activation were identified. By using next-generation high-throughput pyrosequencing and miRNA microarray techniques, miRNAome profiles of Caenorhabditis elegans oocytes (mitotic and meiotic) and early embryos before (2-blastomere stage) and after (8-blastomere stage) zygotic genome activation were generated. Besides observing results similar to those of previous reports, new miRNAs were identified whose expression levels changed during this transformation. After selection and polymerase chain reaction validation of the candidate miRNAs, downstream targets were identified by using bioinformatic tools and they were subjected to pathway analysis. Further analysis of the identified miRNAs in this study may provide a better understanding of the regulation of early embryonic development, germline–soma differentiation, oocyte–embryo transition, and maintenance of totipotency status. © TÜBİTAK.Item Caenorhabditis elegans oosit ve embriyolarında global mikroRNAom profillerinin analizi(Biyoteknoloji Enstitüsü, 2013) Güçlü, Selen; Atalay, Arzu; OtherItem Fibroblast büyüme faktörü 3 (FGF3) geninde tanımlanan L6P ve S156P mutasyonlarının etkilerinin ın vıtro analizi(Biyoteknoloji Enstitüsü, 2010) Başaran, Murat; Atalay, Arzu; BiyoteknolojiHearing loss and deafness are global issues that affect at least 278 million people worlwide. Two third of these people live in developed countries (Tucci vd 2010). Screening of newborns for hearing loss in these countries have shown that congenital hearing loss affects 1,33-1,86 of 1000 children. Hearing loss can occur congenitally or postnatally. Genetic causes account for approximately %50-60 of congenital hearing loss. Approximately 30% of the genetically caused hearing loss is accompanied by other clinical findings and these cases are referred to as syndromic hearing loss (Nance 2003).A new autosomal recessive syndrome with type I microtia (shortening of auricles), microdontia, and profound congenital deafness associated with a complete labyrinth aplasia have been discovered in 2007 (OMIM 610706, LAMM (Deafness with Labyrinthine Aplasia, Microtia, and Microdontia, (Tekin vd 2007)) and it has also been shown that homozygous mutations causing this autosomal recessive syndrome are in the fibroblast growth factor 3 (FGF3) gene (Tekin vd 2008). FGF3 protein, which is encoded by FGF3 gene, is a secreted protein that is expressed at the embryonic stage. In this study, the in vitro effects of two previously identified missense mutations, p.L6P and p.S156P, on secretion of this protein were investigated. After these two mutations were mimiced by site-directed mutagenesis, mutant proteins have subsequently been expressed in cell culture, normal and mutant FGF3 proteins are analyzed for determining the intracellular localization and the quantification. As a result, in contrast to the normal protein, it was found that there have been differences for localization and quantification in mutant FGF3 proteins.Item Genetic diversity of food originated Salmonella isolates(2018) Atalay, Arzu; Biyoteknoloji EnstitüsüCurrently, Salmonella enterica is the most common bacterial foodborne pathogen, causing serious extraintestinal disease. Typing methods play an important role on pathogens’ source tracking, knowing the source(s) of bacteria in pharmaceutical sciences, preventing and controlling the diarrhea and food-poisoning outbreaks. The purpose of this study is to use different moleculer typing methods to determine the genetic variability of 38 foodborne Salmonella isolates that were previously identified by biochemical tests. The methods were evaluated by four molecular techniques including 16S rRNA sequencing, PFGE, PCR-RFLP and invA-spvC PCR. 16S rRNA sequencing results showed that four of the 38 isolates were Escherichia coli, Proteus mirabilis and Citrobacter murliniae, and the others were Salmonella enterica. Thirty-eight strains were subtyped by XbaI-PFGE into 20 profiles with different clusters, while they were subtyped by 16S rRNA-RFLP into 9 profiles with a single cluster. Out of two Salmonella isolates, the invasion gene (invA) was detected in all other Salmonella isolates (94%) and the virulence gene (spvC) was detected in 11% of Salmonella isolates. Our results suggested that the PFGE subtyping is the prominent method for the evaluation and benchmarking of molecular subtyping.Item Integration of in vitro and in silico perspectives to explain chemical characterization, biological potential and anticancer effects of Hypericum salsugineum: A pharmacologically active source for functional drug formulations(2018) Atalay, Arzu; Bender, Onur; Fen FakültesiThe genus Hypericum is one of the most popular genera in both traditional medicine and scientific platform. This study is designed to provide conceptual insights on the biological potential and chemical characterization of H. salsugineum, which is endemic to Turkey. The qualitative and quantitative phenolic content of the extracts was characterized by HPLC-ESI-MSn. Biological efficiency was investigated by enzyme inhibitory assays (cholinesterases, tyrosinase, amylase, and glucosidase) and anti-cancer efficacy tests (anti-proliferative activities with the iCELLigence technology, colony formation and wound healing scratch assays). Phenolic acids (3-O-caffeoylquinic, 5-O-caffeoylquinic, and 4-O-caffeoylquinic acids) were the predominant group in the studied extracts, although several flavonoids were also detected and quantified. The extracts exhibited good inhibitory effects on tyrosinase and glucosidase, while they had weak ability against cholinesterases and amylase. Computational studies were also performed to explain the interactions between the major phenolics and these enzymes. The extracts displayed significant anti-cancer effects on breast carcinoma cell lines. Our findings suggest that Hypericum salsugineum could be valued as a potential source of biologically-active compounds for designing novel products. © 2018 Bender et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Item Integration of in vitro and in silico perspectives to explain chemical characterization, biological potential and anticancer effects of Hypericum salsugineum: A pharmacologically active source for functional drug formulations(2018) Atalay, Arzu; Biyoteknoloji Enstitüsü; Bender, OnurThe genus Hypericum is one of the most popular genera in both traditional medicine and scientific platform. This study is designed to provide conceptual insights on the biological potential and chemical characterization of H. salsugineum, which is endemic to Turkey. The qualitative and quantitative phenolic content of the extracts was characterized by HPLC-ESI-MSn. Biological efficiency was investigated by enzyme inhibitory assays (cholinesterases, tyrosinase, amylase, and glucosidase) and anti-cancer efficacy tests (anti-proliferative activities with the iCELLigence technology, colony formation and wound healing scratch assays). Phenolic acids (3-O-caffeoylquinic, 5-O-caffeoylquinic, and 4-O-caffeoylquinic acids) were the predominant group in the studied extracts, although several flavonoids were also detected and quantified. The extracts exhibited good inhibitory effects on tyrosinase and glucosidase, while they had weak ability against cholinesterases and amylase. Computational studies were also performed to explain the interactions between the major phenolics and these enzymes. The extracts displayed significant anti-cancer effects on breast carcinoma cell lines. Our findings suggest that Hypericum salsugineum could be valued as a potential source of biologically-active compounds for designing novel products. © 2018 Bender et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Item Integration of in vitro and in silico perspectives to explain chemical characterization, biological potential and anticancer effects of Hypericum salsugineum: A pharmacologically active source for functional drug formulations(2018) Bender, Onur; Atalay, Arzu; Biyoteknoloji EnstitüsüThe genus Hypericum is one of the most popular genera in both traditional medicine and scientific platform. This study is designed to provide conceptual insights on the biological potential and chemical characterization of H. salsugineum, which is endemic to Turkey. The qualitative and quantitative phenolic content of the extracts was characterized by HPLC-ESI-MSn. Biological efficiency was investigated by enzyme inhibitory assays (cholinesterases, tyrosinase, amylase, and glucosidase) and anti-cancer efficacy tests (anti-proliferative activities with the iCELLigence technology, colony formation and wound healing scratch assays). Phenolic acids (3-O-caffeoylquinic, 5-O-caffeoylquinic, and 4-O-caffeoylquinic acids) were the predominant group in the studied extracts, although several flavonoids were also detected and quantified. The extracts exhibited good inhibitory effects on tyrosinase and glucosidase, while they had weak ability against cholinesterases and amylase. Computational studies were also performed to explain the interactions between the major phenolics and these enzymes. The extracts displayed significant anti-cancer effects on breast carcinoma cell lines. Our findings suggest that Hypericum salsugineum could be valued as a potential source of biologically-active compounds for designing novel products.Item Lipotoksik endoplazmik retikulum stres sonucu ifadesi değişen mikrornaların tanımlanması ve regüle ettiği genlerin analizi(Biyoteknoloji Enstitüsü, 2014) Nadir, Mısra; Atalay, Arzu; OtherObezite, tip 2 diyabet ve ateroskleroz gibi metabolik düzensizliklerde serbest yağ asitleri, yağ dokusunun yanısıra başka dokularda da birikmektedir. Hücre içindeki serbest yağ asidi birikimine karşı koyamayan -yağ doku harici dokulardaki- hücrelerde Endoplazmik Retikulum (ER) stres ve lipotoksik hücre ölümü gerçekleşir. Katlanmamış Protein Yanıtı (KPY) hücrede biriken serbest yağ asitlerinin endoplazmik retikulumda meydana getirdiği stres durumuna karşı koymak için aktive olan bir mekanizmadır ve hücrenin ER'da oluşan strese karşı koyarak adaptasyonu veya hücrenin kendini apoptoza programlaması arasında anahtar rolü üstlenmektedir. Ancak, uzun süren ve çözümlenemeyen ER stresi, hücreler ve dokular için zararlıdır, ER stresi metabolik dokularda kronikleştigi zaman, metabolik hastalıkların gelişimine yol açmaktadır. Lipotoksisitenin KPY'nı hangi moleküler mekanizmalarla aktifleştirdiği ve KPY sinyal yolağının adaptif veya destrüktif yanıtlarının nasıl kontrol edildiği halen tamamen aydınlatılamamıştır. Son yıllarda tanımlanan ve gelişim, organogenez, kök hücre statüsünün idamesi, kanser gibi biyolojik süreçlerde rol alan mikroRNAların (miRNA), protein kodlayan genlerin yaklaşık %30-60'ını kontrol ettikleri tahmin edilmektedir. Lipotoksik ER stres kaynaklı KPY aktivasyonu sırasında ifadesi değişen miRNAları tanımlamak amacı ile fare makrofaj hücre hattında (RAW 264.7), lipotoksik ER stres oluşturulmuş ve ardından bu hücreler ve kontrol hücre hattının miRNAome profilleri, QRT-PCR temelli miScript miRNA PCR array kullanılarak biyolojik tekrarlı analiz edilmiştir. miRBase 16.sürümdeki tüm fare miRNAları ile yapılan taramada 227 adet miRNAnın ifade seviyesinde değişiklik gözlenmiş, 43 tanesinde 2 kat ve üzeri artma/azalma gözlenirken, 13 adetinde ise 3-24 kat artma/azalma görülmüştür. Lipotoksik ER streste ifadesi değişen bu miRNAların hedef transkriplerini belirlemek için yolak analizleri yardımı ile olası hedef mRNAlar belirlenmiş ve QRT-PCR ile ifade seviyeleri analiz edilmiştir.Item Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis(2008) Atalay, Arzu; Biyoteknoloji Enstitüsü; Boag, Peter R.; Robida, Stacey I.During oogenesis, numerous messenger RNAs (mRNAs) are maintained in a translationally silenced state. In eukaryotic cells, various translation inhibition and mRNA degradation mechanisms congregate in cytoplasmic processing bodies (P bodies). The P body protein Dhh1 inhibits translation and promotes decapping-mediated mRNA decay together with Pat1 in yeast, and has been implicated in mRNA storage in metazoan oocytes. Here, we have investigated in Caenorhabditis elegans whether Dhh1 and Pat1 generally function together, and how they influence mRNA sequestration during oogenesis. We show that in somatic tissues, the Dhh1 orthologue (CGH-1) forms Pat1 (patr-1)-dependent P bodies that are involved in mRNA decapping. In contrast, during oogenesis, CGH-1 forms patr-1-independent mRNA storage bodies. CGH-1 then associates with translational regulators and a specific set of maternal mRNAs, and prevents those mRNAs from being degraded. Our results identify somatic and germ cell CGH-1 functions that are distinguished by the involvement of PATR-1, and reveal that during oogenesis, numerous translationally regulated mRNAs are specifically protected by a CGH-1-dependent mechanism. © 2008 Boag et al.Item RNA interference and current clinical applications: Review(2016) Atalay, Arzu; Biyoteknoloji Enstitüsü; Bender, Onur; Çelebi, EvrimRNA interference (RNAi), which is one of the technological breakthroughs of modern biology not only became an important tool for gene function analysis in eucaryotes, but also being used as a promising technology for therapeutic gene silencing studies. The importance of this mechanism, which was described in almost all eukaryotic organisms, is reflected by the fact that the 2006 Nobel prize for medicine was awarded for the discovery of RNA interference by Craig Mello and Andrew Fire. Both microRNAs and siRNAs use RNAi machinery in order to be processed and being functional resulting in gene silencing via degraded or translationally repressed mRNA and no protein synthesis. During the last 15 years, a greater understanding of RNAi mechanism, the intracellular actioning, modifications for stable siRNAs and nanocarrier systems for delivery, presents siRNA therapeutics as an attractive newclass of therapeutics, especially against undruggable targets for the treatment of cancer and other diseases. According to American National Health Institute, there are many ongoing clinical trials with RNAi drugs. Current clinical studies are focused on developing therapies for the treatment of cancer, infection diseases, ocular conditions, cardiovascular and metabolic diseases, genetic diseases and a few other diseases. The drugs for the disease genes are designed in a way to reach to spesific tissue with high yield using carrier systems in order to achieve optimal efficiency. Thus, RNAi based drugs are expected to be an effective therapy system in near future, with ongoing active clinical applications. In this review, some of the ongoing clinical phase studies with siRNA therapeutics are summarized. © 2016 by Türkiye Klinikleri.Item Traditionally used lathyrus species: Phytochemical composition, antioxidant activity, enzyme inhibitory properties, cytotoxic effects, and In Silico studies of L. Czeczottianus and L. Nissolia(2017) Atalay, Arzu; Biyoteknoloji Enstitüsü; Bender, Onur; Uysal, SengülMembers of the genus Lathyrus are used as food and as traditional medicines. In order to find new sources of biologically-active compounds, chemical and biological profiles of two Lathyrus species (L. czeczottianus and L. nissolia) were investigated. Chemical profiles were evaluated by HPLC-ESI-MSn, as well as by their total phenolic and flavonoid contents. In addition, antioxidant, enzyme inhibitory, and cytotoxic effects were also investigated. Antioxidant properties were tested by using different assays (DPPH, ABTS, CUPRAC, FRAP, phosphomolybdenum, and metal chelation). Cholinesterases (AChE and BChE), tyrosinase, a-amylase, and a-glucosidase were used to evaluate enzyme inhibitory effects. Moreover, vitexin (apigenin-8-C-glucoside) and 5-O-caffeoylquinic acid were further subjected to molecular docking experiments to provide insights about their interactions at molecular level with the tested enzymes. In vitro cytotoxic effects were examined against human embryonic kidney cells (HEK293) by using iCELLigence real time cell analysis system. Generally, L. czeczottianus exhibited stronger antioxidant properties than L. nissolia. However, L. nissolia had remarkable enzyme inhibitory effects against cholinesterase, amylase and glucosidase. HPLC-ESI-MSn analysis revealed that flavonoids were major components in these extracts. On the basis of these results, Lathyrus extracts were rich in biologically active components; thus, these species could be utilized to design new phytopharmaceutical and nutraceutical formulations. © 2017 Llorent-Martínez, Zengin, Fernández-de Córdova, Bender, Atalay, Ceylan, Mollica, Mocan, Uysal, Guler and Aktumsek.Item Türk halk ilaçlarının C.elegans ömür uzunluğu üzerine etkisinin araştırılması(Biyoteknoloji Enstitüsü, 2012) Ergen, Nuri; Atalay, Arzu; BiyoteknolojiAging is a process, which contributes to the functional loss of an organism and ultimately carries it to death with the passage of time. For many years, medical science, is working to improve the quality of life. In addition to improving the quality of life, increasing the maximum life expectancy was also intended. The incidence of age related diseases such as obesity, diabetes, atherosclerosis, cancer, Parkinson's disease, Alzheimer and depression was observed to be increased with the improvement of life quality and increase in life expectancy. Research in the field of aging is getting important not only it is related to the prolongation of life expectancy, but also related to prevention of the diseases that occur with aging.The use of model organisms is quite common for the elucidation of biological processes. Caenorhabditis elegans is a model organism that is commonly used in aging studies since its genome is well-known, it shows 60-80% homology with human genome, can be easily manipulated in laboratory conditions and it has nearly 20 days of survival time.As it is well known that vast majority of the drugs are obtained from plant sources. There is a high probability of developing a drug candidate molecule from a plant used as a folk medicine. Turkey has a very rich flora most of which are endemic and has a rich folk medicine culture. The purpose of this study is to investigate the effects of Turkish folk medicines to aging and some age related diseases. 12 plant extracts with antidiabetic and antibacterial activities, which are believed to be panacea, were chosen form previously reported folk medicine inventory studies and their effects on C. elegans longevity was investigated. Additionally, some pathway analysis was also conducted with the experiments performed with mutant strains.