Browsing by Author "Duman, Demet Cansaran"
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Item Evaluation of different isotherm models, kinetic, thermodynamic, and copper biosorption efficiency of Lobaria pulmonaria (L.) Hoffm(2013) Duman, Demet Cansaran; Biyoteknoloji Enstitüsü; Kılıç, Zeynep; Aras, Sümer; Atakol, Orhan; Çelikkol, Pelin; Emregul, EmelItem Evaluation of the impact on different types of human cancer cell of lichen secondary compounds(2013) Yılmaz, Erkan; http://orcid.org/0000-0001-7355-3878; Dil ve Tarih-Coğrafya Fakültesi; Özenoǧlu, Sinem; Taghidizaj, Afşar Abbasi; Duman, Demet CansaranToday, cancer is appearing as a major unsolved health problem. Basicly, surgery, chemotherapy and hormone therapy models are used in the treatment of cancer. Basic procedures and drugs used in the treatment of cancer are thought to be insufficient. These treatments have some side effects and they take a long time. Due to the problems encountered in the treatment of cancer in the recent years, alternative methods of treatment are being researched. For this purpose the effect of herbal, synthetic and fungus organisms against various types of cancer is being investigated. As a result of these investigations, lichens and their secondary metabolites are also proposed to be used as an alternative method in cancer treatment. Lichens are a symbiotic association of a fungus and a photosynthetic partner. These metabolites were identified as fatty acids, lactons, zeorin, pulvic acid, petroleum, depsids, depsidons and antrokinon derivatives. Impact of lichen secondary compound studies on different human cancer types, aims to find a promising drug Candidate molecule.Item Heavy metal accumulation of five biomonitor lichen species in the vicinity of the karabük iron and steel factory in karabük, Turkey and their comparative analysis(2012) Duman, Demet Cansaran; Aras, Sümer; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji EnstitüsüObjective: To investigate the suitability of five biomonitor lichen species (Evernia prunastri, Hypogymnia physodes, Pseudevernia furfuracea, Ramalina pollinaria and Usnea hirta) that were collected from Yenice Forest to the Karabük Iron and Steel Factory in Karabük, Turkey, from 10 sites. Method: Each of the five biomonitor lichen species was collected from every 5 kms starting from Yenice forest to iron steel factory. Accumulation of eight heavy metals Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn in examined lichen species were analyzed by Atomic Absorption Spectrophotometer (AAS). Results: We have compared the capacity of five biomonitor lichen species to accumulate trace elements from the atmosphere which were collected from around the Karabük Iron and Steel Factory in Karabük, Turkey. Sites 1, 2, 7 and 10 were in the central parts of the city where human activities and density of traffic are very intense. Analytical studies by AAS demonstrated that the heavy metal accumulation capacity of P. furfuracea was significantly higher than other examined lichen species at sites 7 (40.628 μg/g) and 10 (53.802 μg/g) by considering Zn accumulation. At the site no 8, Cr concentrations of H. physodes (4.56 μg/g) and E. prunastri (4.65 μg/g) were observed at similar levels. Conclusion: Our results revealed that, Evernia prunastri, Hypogymnia physodes, Pseudevernia furfuracea, Ramalina pollinaria and Usnea hirta lichen species showed severe accumulation of all elements. This study demonstrated the importance of heavy metal accumulation in the selected lichen species.Item Identification of some Lecidea, Porpidia and Lecidella species (lichen-forming ascomycetes) distributed in Turkey by sequence analysis of rDNA ITS region(2015) Duman, Demet Cansaran; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji Enstitüsü; Başaran, Esin; Büyük, Ilker; Aras, SümerObjective: The taxonomy of Lecidea is extremely complex because of the enormous morphological variation within and between species. The aim of this study was to analyse the rDNA (ITS) regions of Lecidea species and related genus called Lecidella and Porpidia which are widely spreaded in Anatolia, Turkey. Methods: The ITS rDNA sequence information of 17 samples from 11 species which were collected from different provinces of Anatolia were generated. Some of the specimens from Lecidea, Lecidella, Lecanora and Porpidia genus were also taken from the GenBank (www.ncbi.nlm.nih.gov). The phylogenetic analysis was performed by the help of four different methods (NJ, ME, MP, UPGMA) and these different methods manifested similar results. Results: Minimum-Evolution (ME) dendrogram revealed that species of Lecidea, Lecidella, Porpidia and Ganoderma sp. genus were distributed into four main branches. Ganoderma applanatum (GU256764) which was considered as outgroup formed one of the branches, while the other species were collected on the other branchs. Generally the species which belong to the same genus, combined in one branch towards to the origin. In accordance with the results derived from molecular phylogenetic analysis, genus Lecidea is found closer Porpidia rather than Lecidella morphologically. Numerable 4100 nucleotides were obtained from DNA sequences of related region of studied samples. It was indicated that 177 nucleotides of those regions were stable (C), 747 nucleotides were variable (V). It was confirmed that there were transitions in 56 nucleotide pairs, tranversion in 54 nucleotide pairs of compared samples. Conclusion: In this study, the results of phylogenetic analysis of the genus Lecidea and other similar groups were firstly evaluated and the results will not be only a guide but also will provide a resource for next researchers.Item Industrial and biotechnological applications of laccase enzyme(2015) Duman, Demet Cansaran; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji Enstitüsü; Demiralp, Begüm; Büyük, Ilker; Aras, SümerEnvironmental pollution had emerged by the beginning of urban life and increased parallel to the industrial development. Rapidly increasing industrial activities, dumping of the wastes to the environment by the factories and releasing of the toxic chemicals have adverse impact on human health. Due to their ability to oxidise a wide range of substrates, which makes laccases very useful biocatalysts for their application to different industrial and biotechnological areas in recent years. Laccase enzyme is used in enhancing appearance color of the foods and drinks, in seperating lignin from paper and paper pulp and removing lignin from paper pulp, in textile industry as a colourant, bleaching of textile products, denim washing, various boiling processes, biological degradation and discoloration of textile waste waters, in different industries such as bioremediation and cosmetic industries and in biotechnology applications as biocatalyst. Laccase enzymes are obtained mainly from fungi and various types of organisms. In today's conditions laccase enzyme are not obtained cheaply and easily for use in the industrial field. Surplus amount of laccase enzyme production is required for the bioremoval of the contaminated zones especially in industrial areas. To find the most effective laccase-producing source, it is required to choose the most appropriate fungal type, to find out the regenerative and inexpensive isolation methods or to optimize the enzyme production conditions.Item Meme kanseri tedavisinde miR-185-5p''nin etkinliğinin proteomikyaklaşımla belirlenmesi(Biyoteknoloji Enstitüsü, 2019) Torun, Vildan; Duman, Demet Cansaran; BiyoteknolojiMeme kanseri dünya genelinde kadınlar arasında en yaygın görülen kanser tipleri arasındadır. Kanserin tedavisinde kemoterapi, radyoterapi ve cerrahi yöntemler yaygın olarak kullanılmaktadır. Tedavi amaçlı kullanılan her bir yöntemin kendine özgü avantaj ve dezavantajı vardır. Kanser hastalığının kişiye özgü bir hastalık olması, tedavinin kişiden kişiye farklılık gösterebilmesi nedeniyle son yıllarda farklı alternatif tedavi araştırmaları artmaktadır. Yapılan araştırmalar sonucunda kanser tedavisinde miRNA'ların yeni nesil biyoişaretleyici ve terapötik ajan olma potansiyelini ortaya çıkarmışlardır. Meme kanseri tedavisinde rutin olarak kullanılan Tamoksifen ve Lapatinip gibi ilaçlara karşı cevap oluşturan ve tedaviye karşı etkinliği belirlenen miRNA'lar son yıllarda kanser araştırmalarının odak noktası olmuştur. Doğada yer alan biyolojik organizmalardan biri olan likenlerden elde edilen usnik asit sekonder metaboliti, rutin tedavide kullanılan ilaçlar kadar aday bir molekül olduğu belirlenmiştir. Gerçekleştirilen öncül çalışmada usnik asitin üç farklı meme kanseri hücreleri üzerine uygulaması sonucunda; BT-474 meme kanser hücresine karşı cevap veren miRNA'lar içinde qRT-PCR'a dayalı validasyon çalışmaları sonucunda ve biyoinformatik temelli yaklaşımlarla değerlendirmeler sonucunda meme kanseri ile ilişkili yolaklarda işlev gösterdiği belirlenen miRNA miR-185-5p'dir. Protein yapısındaki bozulmalar yolakların işlevsel özelliklerinde dejenerasyona neden olmaktadır ve nihai olarak da bu durum kanser hastalığına neden olmaktadır. Genlere göre daha etkin fonksiyonel özellik gösteren proteinlerin işlevselliğinin belirlenmesi çalışmaları kanser tedavisinde etkin çözüm arayışında önemli bir adımdır. Gerçekleştirilen tez kapsamında meme kanseri (BT-474) ve normal meme doku hücrelerinde (MCF-12A) usnik aside cevap veren miR-185-5p mimik uygulaması sonrasında protein düzeyindeki farklılaşmalar Sıvı kromotografisi/Kütle Spektrometresi (LC-MS/MS) tabanlı proteomik yöntemle belirlenmiştir. Hücrelerden izole edilen protein örnekleri, nano-LC-MS/MS ile tanımlanarak karşılaştırmalı proteomik analize tabi tutulmuştur. Analiz sonucunda 858 tane protein tanımlanmış olup, meme kanseri ve normal meme hücreleri arasında 86 tanesinin ifadesinde anlamlı bir farklılık bulunmuştur. Bu proteinlerden 53 tanesinin ifadesinde artış, 33 tanesinin ifadesinde azalma olduğu tespit edilmiştir. Çalışma sonucunda BT-474 meme kanseri hücresine miR-185-5p mimik uygulaması ile ifade değişimi gösteren proteinler YWHAE, PAK1 ve Katepsin D proteom boyutunda tespit edilmiştir. Elde edilen sonuçlarla, proteinlerin meme kanseri hastalığındaki rolünün belirlenmesi ve meme kanserine karşı hedeflenmiş miRNA temelli tedavi yöntemlerinin proteom boyutunda karakterizasyonu sağlanmıştır.Item Pharmaceutical applications based on next generation sequencing technology in oncologic drug development(2019) Duman, Demet Cansaran; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji Enstitüsü; Yangın, Sevcan; Tanman, ÜmmügülsümIn order to find an effective solution to the treatment of cancer disease, many international collaborative researches have been carried out and many promising results have been obtained from these on going studies. An effective solution has not yet been found for cancer disease but studies on the development of new treatment methods and the findings of the research results continue to be published. In this context, in the studies focusing on the treatment of cancer, the findings obtained after the use of advanced technologies have been used in personalized medicine and clinical applications. Nowadays, next-generation sequencing technologies, which provide information on genomes with genome sequencing, are one of the most advanced technologies used in cancer research. Next-generation sequencing technology examines both genes and identifies some mutations. This technique enables the identification of unknown sequence variations in a short time and more easily, thus enabling clinicians to better understand the mechanisms of cancer. In this review, we aimed to provide information about the availability of next generation sequencing technology in pharmaceutical applications including areas such as tumor marker determination to pharmacogenomics, targeted therapy, precision medicine, vaccine treatment, biopharmaceutics, polypharmocology, toxgonostics and pharmacoepidemiology.Item Pharmacogenomics in lung cancer treatment(2017) Duman, Demet Cansaran; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji Enstitüsü; Kılıç, NilLung carcinoma is the most common cause of cancer-related death in men among other cancer types in last years. The most recent and significant step in the treatment of the disease is the determination of the human genome structure and understanding of tumor biology. Pharmacogenomics examines tumordependent gene mutations to determine in which patient the drug will be more effective. Personalized treatments that are specified directly to disease by using pharmacogenomics methods are applied to cure patients with minimum side effects. Also, determining sensitivity of drug against tumor by examining gene mutations in patients plays a crucial role in selection and outcome of treatment. Patient-specific pharmacogenetic applications in lung carcinoma treatment and their effects on prognostic of disease were reviewed in this study.Item RNA interference in plants(2015) Duman, Demet Cansaran; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji Enstitüsü; Aras, Sümer; Aydın, Semra Soydam; Fazlioğlu, Asli; Büyük, Ilker; Derici, KürşatRNA interference (RNAi) is defined as silencing of gene after transcription (post-transcriptional gene silencing), when double stranded RNA (dsRNA) steps into the cell and cause degradation of endogenic complementary mRNA, or regulation of gene expression process. During RNA is mechanism, complementary sequence of target mRNA connects to sense strand of mRNA by factor of RISC. Gene silencing mechanism is controlled by RISC factor with a mass of 500 kDa which is RNA multi protein complex with nuclease activity. Silencing is occurred by cutting of mRNA, which is interacting with Argounate protein on RISC factor, with Dicer enzyme. This silencing mechanism is natural and takes a position in defending genome and biological function of organisms from invasion of movable genetic material such as viral hereditary material and transposons. RNAi mechanism realized with two kinds of molecules in eukaryotic organisms. These are miRNA (microRNA) which is 22 bp and siRNA (small interfering RNA) which is 21-23 bp. In recent years RNAi has become prominent research area in science world. Several information were achieved with researches of RNAi such as determining function of genes, host-pathogen interaction, reproduction, apoptosis (programmed cell death) and tumorgenesis etc. Also, determined with RNAi researchs that; non-coding RNA plays role in controlling of tissue development and differentiation, signal transduction, interaction with phytohormone, responses of abiotic (drought, salinity etc.) or biotic (pathogens etc. ) stress. As a conclusion, this review will try to explain base of RNAi mechanism and usage in plants. SciVal Topic Prominence Topic: Gene Silencing | Viruses | Rattle virus Prominence percentile: 78.052 Author keywords miRNAPlantRNAisiRNA ISSN: 03779777 Source Type: Journal Original language: English, Turkish DOI: 10.5505/TurkHijyen.2015.13285 Document Type: Review Publisher: Refik Saydam National Public Health Agency (RSNPHA) References (57) View in search results format All 1 Napoli, C., Lemieux, C., Jorgensen, R. 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(2008) Agricultural Sciences in China View all related documents based on references Find more related documents in Scopus based on: Authors KeywordsItem The molecular mechanisms of the effect of anticancer activity on lichen metabolites(2017) Duman, Demet Cansaran; http://orcid.org/0000-0001-5662-2333; Biyoteknoloji Enstitüsü; Şekerli, Merve; Kılıç, NilThe components obtained from natural products have been used in many fields such as medicine, pharmacy and biology throughout the history. Some important new commercial drugs have been obtained from natural molecule using as a model in the cancer field. Studies for the development of cytotoxic agents were an important step for the discovery of new anticancer drugs. Large structural diversity of natural components and their bioactivity potential may serve to improve the therapeutic potential with molecular modification. The number of studies on the anticancer activity of lichen components has increased in last few years. Lichens are symbiotic organisms of fungus and algae or cyanobacteria. Lichens synthesize a great variety of secondary metabolites. Lichen secondary compounds have many possible biological activities such as antiviral, antitumor, antibacterial and antiherbivore and antioxidants. In recent years, one of the most important features of lichen secondary metabolites will also be candidate molecules in the treatment of anticancer therapy in the medical and biotechnology studies. Elucidation of the molecular basis of cancer related processes and also apoptosis pathway are provide to great utility in finding alternative drugs for treating cancer. In this review research the knowledge about lichen secondary metabolites, the potential for effective use in the treatment of cancer, all molecular mechanisms in cancerous processes and mainly apoptosis pathway.Item Usnic acid causes apoptotic-like death in Leishmania major, L. infantum and L. tropica(2018) Duman, Demet Cansaran; Biyoteknoloji EnstitüsüLeishmaniasis, a deadly parasitic infection, threatens many people worldwide. Since the high cost, toxicity, and resistance are drawbacks of current treatment options, it is necessary to find safer and more effective new antileishmanial drugs. The aim of this study was to determine the antileishmanial activity of usnic acid and its apoptotic mechanism on Leishmania spp. promastigotes. The antileishmanial activity was evaluated by MTT assay and apoptosis-related gene expression was investigated by qRT-PCR. Usnic acid was to be effective against Leishmania major, L. infantum, and L. tropica promastigotes at IC50 = 10.76 µg/ml, 13.34 µg/ml, and 21.06 µg/ml, respectively. We also demonstrated a novel mechanism by which usnic acid inhibited proliferation and caused apoptosis; usnic acid upregulated p53, Bax, Casp-3, and Casp-9 gene expression and downregulated the level of Bcl-2 gene expression. Accordingly, the expression level of the P53 gene increased in L. major, L. infantum and L. tropica by 14.4-, 11.8-, and 9.5-fold, respectively, and in contrast, the Bcl-2 gene expression decreased in all three leishmaniasis by 0.8-, 0.8-, and 0.7-fold, respectively. The present study, therefore, revealed that usnic acid played a critical role in the usnic acid-induced apoptotic process in Leishmania species. Usnic acid is easily accessible and an inexpensive agent, and can be considered as an alternative therapeutic agent for Leishmania infections subject to further tests in animal modelsItem Usnik asit liken sekonder metabolitinin farklı kanser hücre tipleri üzerine etkisinin araştırılması(Biyoteknoloji Enstitüsü, 2016) Dinçsoy, Adnan Berk; Duman, Demet Cansaran; BiyoteknolojiNowadays cancer is an important public health problem and presence of undesirable side effects of cancer drugs that is often used in the treatment of cancer has stimulated the search for alternative therapeutic approaches. Therefore anticarcinogenic effects of synthetic, herbal and fungal origin drugs have been investigated against various types of cancer in recent studies. Lichens, symbiotic organisms consisting of fungi and algae and synthesize metabolites with many biological activities. As a result of research, lichens and their secondary metabolites to be used as an alternative biological organisms is suggested to be a solution for treating cancer. In the current study, screening of the anticancer effect potential of usnic acid (UA) on various types of normal (L929 and Vero) and different cancer cell line (CaCo2, HepG2, Hep2C, RD and Wehi) were investigated. The cells were treated for 24, 48 and 72h by UA at final concentration 6.25, 12.5, 25, 50, 100, 200 and 400uM. The growth inhibitory effect of UA were determined by MTT assay. Furthermore, this study was to explore mRNA expression profiles because inhibition of UA might be related to apoptotic pathway. This is the first study that explains antiproliferative effects of usnic acid on cancer and normal cells at a level of mRNA by qRT-PCR. The effect of UA on the gene expression pattern of the tumor suppressor gene TP53, Bcl and BAX- 2 were studied with qRT-PCR. Our results revealed that, 6.25 and 12.5 uM doses of UA have significant cytotoxic effect on examined cancer cell lines. Our present results suggest that usnic acid plays a major role in the regulation of apoptosis in cancer cells. The obtained finding is foreseen that lichen metabolites as UA improves cancer response to cancer treatment in patients resistant to routine chemotherapy provides supportive effect. Further study is required to enlighten additional molecular mechanisms depend on the anti-cancer activity of the lichen species and their secondary metabolites.Item Yaylacık araştırma ormanı (Karabük-Yenice) liken florası(Fen Bilimleri Enstitüsü, 2007) Duman, Demet Cansaran; Yurdakulol, EnderBu çalışmada Bolu ve Karabük illeri içerisinde yer alan Yaylacık Araştırma Ormanı ve Yenice Ormanlarını inceleyerek biyoçeşitliliğinin belirlenmesi amaçlanmıştır. Çalışma bölgesinde, 2003-2005 yıllarında 47 lokaliteden toplanan liken örnekleri değerlendirilerek 142 liken ve 8 likenikol mantar taksonu tanımlanmıştır. Bu taksonların deskripsiyonları, çalışma alanı, ekolojik özellikleri, Türkiye ve Dünya' daki yayılışları verilmiştir. Teşhis edilen 4 liken ve 3 likenikol mantar taksonu Buellia schaereri De Not., Caloplaca cretensis (Zahlbr.) Wunder, Echinothecium reticulatum Zopf, Lichenoconium pyxidatae (Ach.) Ach., Rinodina septentrionalis Malme, Toninia pennina (Schaer.) Gyeln. ve Zwackhiomyces lecanorae (Stein) Nik. Hoffm. & Hefellner Türkiye için yeni kayıttır. Çalışma alanında bulunan liken ve likenikol mantar türlerinden 71'i Bolu için, 145 tanesi Karabük için yeni kayıttır.