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Öğe Sıçan peritoneal endometriozis modelinde metformin ve OTX008’in etkisi: Galektin ve sinsitinlerin payı(2023) Taner Dastan; pelin koparır; Sevgi Durna DAŞTAN; seda ilkin can; ali çetin; mustafa özkaracaSıçan peritoneal endometriozis modelinde metformin ve OTX008’in etkisi: Galektin ve sinsitinlerin payıÖğe COLLABORATİVE CLİNİCAL RESEARCH ON METABOLOMİCS(2023) Sevgi Durna DAŞTAN; Taner DastanCollaborative Clinical Research on Metabolomics Because the significance of metabolomics science and clinical trials increases day by day. Some diseases like cancer is an important cause of mortality for which no definitive treatment has yet been found. Further investigation of the relationship between metabolomics and diseases will open new horizons for diagnosis and treatment of many kind of diseases. This project presents all about metabolomics from the beginning to the end, as many kind of studies, potential mechanisms, diagnosis techniques, the metabolomics technologies like GC-MS, LC-MS, and software programmes about metabolomics analysis. Every researcher collected some part of metabolomics science.Öğe The Concepts of Epigenomics and Cell Epigenomes(Published by Nova Science Publishers, Inc. † New York, 2023) Taner Dastan; İnanç BaralAbstract Genetics cannot solely explain genetic variations in humans and disease developments. We see varying differences in phenotypes and disease susceptibility in organisms that have the same genetic make-up, e.g., monozygotic twins and cloned animals. The information carried by the genomic sequence is the blueprint, but the final product requires environmental determinants. Here comes the concept of epigenetics, as it is the framework where biochemical interactions between the genome and the environment blend. We can describe epigenetics as mechanisms that are beyond genetics, as such mechanisms alter the result of the genomic blueprint without altering the information itself, i.e., the sequence. Both epigenetics and epigenomics are trending research fields to better evaluate the genotype and the phenotype. The methylation of genetic material is a well-studied and well-known epigenetic marker. The epigenome, as a term, describes the inheritable changes in both the DNA and histone molecular structures, where the methylation and acetylation mechanisms are studied extensively. As the building blocks of the chromatin structure, nucleosomes depend on epigenetic changes, which lead to becoming either tight or loose, based on the particular mechanisms. Chromatin structure changes directly affect the gene expression, e.g., particular gene expression becomes silenced if the gene position has DNA hypermethylation and histone hypoacetylation that leads to the condensed form of the chromatin. Inversely, if the said changes were removed, genes in that position would express themselves again. Therefore, epigenetics provides a vigorous and remarkably malleable means for gene expression regulations. Epigenomics includes both the epigenetic mechanisms on the DNA and histones and complicated interactions between the genotype and the phenotype. There are well-known epigenomic changes in DNA, RNA, and protein levels. DNA base changes in somatic cells and chromosome positioning are among the aspects determining the epigenomic scene. Alternative splicing mechanism, RNA processing (editing, capping, Poly-A tailing, etc.), RNA methylation, and regulations conferred by the non-coding RNAs (ncRNAs) are RNA level epigenomic changes. Epigenomic changes at the protein level include various mechanisms of the post-translational modification.Öğe TRANSGENİK BİTKİ TÜRLERİ İÇİN İLGİLİ KARAKTER VE GENLER: İŞARET GENLERİ VE PROMOTÖRLER(L,vre de Lyon, 2023) İnanç Baral; Taner DastanTransgenik bitki araştırmaları, istenen özellikleri kazandırmak için bitki türlerine yeni genlerin eklenmesini mümkün kılarak tarım alanında devrim yapmıştır. Bu bölümde transgenik bitki araştırmalarının temel yönlerine genel bir bakış sunulmuş ve özellikle promotor ve işaretçi genlerin kullanımına odaklanılmıştır. Promotorlar, gen ifadesini düzenlemede kritik bir rol oynar ve bitkilerin dokuya özgü ifadesi, uyarılabilir gen düzenlemesi ve transgenik bitkilerde artan stres toleransı sağlamak için farklı tipte promotorlar, örneğin floem özgül promotorlar, stres uyarılabilir promotorlar ve RuBisCo küçük alt birim promotorları gibi birçok tür kullanılmıştır. Neomisin fosfotransferaz II (nptII), yeşil floresan protein (GFP) ve β-glukuronidaz (GUS) gibi işaretçi genler, transgenik bitkilerin tanımlanması, seçilmesi ve karakterize edilmesinde önemli rol oynamıştır. Bu işaretçi genler, gen ifadesi desenlerinin, dokuya özgü ifadesinin ve hücresel lokalizasyonun izlenmesini kolaylaştırmıştır. Ayrıca, çevresel riskleri azaltma ve düzenleyici onayı kolaylaştırma konularıyla ilgili endişeleri ele almak için seçilebilir işaretçi genlerin varlığı ile ilgili alternatifler olarak, işaretçisiz stratejiler ortaya çıkmıştır. Cre/lox veya FLP/FRT gibi site özgü rekombinasyon sistemlerini kullanarak, işaretçisiz transgenik bitkiler oluşturulabilir, çevresel riskleri azaltabilir ve düzenleyici onayı kolaylaştırabilir. Promotor ve işaretçi genlerin birleşimi, transgenik bitki araştırmalarını önemli ölçüde ilerletmiştir, böylece artan stres toleransı, daha iyi böcek direnci ve artmış verim gibi iyileştirilmiş özelliklere sahip genetik olarak değiştirilmiş ürünlerin geliştirilmesini mümkün kılmıştır.Öğe Determination of oxidative stability of different vegetable oils by means of middle infrared spectroscopy and DFT calculations(Microchemical Journal, 2023) Ayse Burcu Aktas; Taner Dastan; Konstantin P. Katin; Savas KayaOxidative stability is one of the most important quality parameters of vegetable oils. This study aims to determine oxidative stability of five different vegetable oils by means of infrared spectroscopy combined with DFT calculations and to compare experimental and theoretical results. The oxidation induction times of hazelnut, corn, canola, safflower and sunflower oils were determined by the Rancimat method and fatty acid profile of the oils was analyzed by gas chromatography. Moreover, the middle infrared spectra of the samples was obtained by using Fourier transform infrared spectroscopy. The oxidative stability of the vegetable oils was analyzed by considering two mechanisms regarding to oxidation process in the theoretical parts of the study. The chemical hardness of fatty acids, a key characteristic of Conceptual Density Functional Theory, was calculated and discussed. It was evaluated that there was a remarkable correlation between oxidative stability and chemical hardness of fatty acids. The harder fatty acids had stronger oxidative stability. A new, accurate, cost-effective, and ecologically friendly technique was developed for determination of oxidative stability of vegetable oils.Öğe Immobilization of pectinase on chitosan-alginate-clay composite beads: Experimental, DFT and molecular docking studies(Elsevier, 2023) Aksu, Aysun; Çetinkaya, Serap; Yenidünya, Ali Fazıl; Çetinus, Şenay Akkuş; Gezegen, Hayreddin; Tüzün, BurakPectinase was immobilized on chitosan-alginate-clay (CAC) beads using epichlorohydrin (ECH) as the crosslinker. Prepared beads and immobilization product were analyzed by Fourier Transform Infrared Spectrophotometry (FTIR) and Scanning Electron Microscopy (SEM). Experimental data covered some hydrolytic properties of the immobilized enzyme, such as pH, temperature, reusability, concentration, and storage time. The immobilization procedure increased the optimal temperature to 60 ◦C and maximum activity was obtained at pH (6.0). After 5 cycles of reuse, approximately 45% of the initial activity of the immobilized enzyme remained. Free pectinase, CAC, and immobilization product were also investigated by Gaussian calculations, the HF/6-31g basis set. Furthermore, Aspergillus niger proteins (PDB ID: 3K4P and 7BLY) and Staphylococcus aureus (PDB ID: 1JIJ) were examined for molecular docking calculations, and ADME/T calculations were made to examine the effects and reactions of these molecules in human metabolism.Öğe Optimization of Spontaneous Fermentation Conditions of Kohlrabi by Response Surface Methodology(MDPI, 7 Haziran 2023) Aktaş, Ayşe BurcuKohlrabi is a valuable crop due to its substantial amount of macro- and micronutrients. It is mostly consumed in fresh form, as jam or fermented product. This current work aimed to optimize the spontaneous fermentation conditions of kohlrabi in order to improve its product functionality and diversity. For this purpose, a Box Behnken design was employed to evaluate the effects of boiling time (0–8 min.), vinegar ratio (0–50%), and salt content (2–8%) on chemical and microbiological properties of fermented kohlrabi. Some chemical and microbiological analyses, including total phenolic content, total antioxidant capacity, total acidity, pH, salt content, total counts of yeast and molds, and mesophilic and lactic acid bacteria, were determined. The total antioxidant capacity of samples changed between 11.91 and 75.75 µmol Trolox/100 g, respectively. Both ANOVA results (p < 0.05) and PCA model (R2 = 0.99; Q2 = 0.72) confirmed that boiling time is the important factor affecting the fermentation process. The optimal fermentation parameters for kohlrabi were determined to be 44.12% vinegar and 2.07% salt concentrations without the boiling step by response surface methodologyÖğe Enrichment of green table olives by natural anthocyanins during fermentation(Springer, 26 Nisan 2023) Aktaş, Ayşe BurcuThe aim of this study is the enrichment of green table olives with anthocyanins by using beetroot and black carrot in the fermentation media and to improve functional properties of fermented olives. For this purpose, a full factorial design was constructed by considering the fermentation time, vegetable type and vegetable concentration as processing factors. The changes in the chemical and microbiological properties of both olive and brine samples were monitored. During fermentation, while phenolic components of olives were transferred to the brine, the anthocyanins originating from the black carrot and beetroot difused into both olive and brine samples. The total monomeric anthocyanin content of fermented olives containing 20% percent of black carrot and beetroot was 149.87 and 154.05 mg/kg respectively. Moreover, the color of olives turned as fermentation progressed. Both ANOVA results (p<0.05) and PCA model (R2=0.99; Q2=0.93) confrmed that reaction time is most important factor for the fermentation process. The sensorial analysis results indicated that the olives fermented with 20% vegetable for 10 days had been highly scored by panelists.Öğe Fourier transform infrared spectroscopy and chemometrics for chemical property prediction of chemically interesterified lipids with butterfat and vegetable oils during storage(Elsevier, 15 Şubat 2023) Aktaş, Ayşe BurcuThe storage stability of structured lipids has a great importance for food industry and should be defined clearly. The aim of the study is to manufacture structured lipids by chemical interesterification of butterfat with different vegetable oils, to determine some chemical properties of interesterified lipids throughout storage and to predict free fatty acid, peroxide value, malondialdehyde and mono-di-triacylglycerol contents of these lipids by using middle infrared spectroscopy (FT-MIR). Prediction models were constructed by using partial least square (PLS) regression with an external cross-validation. The PLS model for TAG with FT-MIR data showed an excellent predictive potential with higher R2 cal=0.98, R2 cv=0.99 and lower RMSE values. The model for monoacylglycerol content (MAG) showed a good predictive ability with higher R2 cal=0.88, R2 cv=0.90 and lower RMSE values. The PLS model constructed with FT-IR spectra for diacylglycerol (DAG) content have good capability of prediction due to higher R2 and lower RMSE values. For the prediction of malondialdehyde (MAD) of interesterified lipids by FT-MIR spectra, regression coefficient of calibration set was found as 0.84. For the prediction of peroxide value (PV) of interesterified lipids with FT-MIR spectra, R2 CV=0.76 and RMSEC=1.52 and RMSECV=1.15. Infrared spectroscopy technique could be used for analyzing the chemical changes of fats during storage and also suggests a rapid and non-destructive techniques as good alternatives to the traditional analytical methods.Öğe Wild-type IDH1 Knockout Leads to G0/G1 Arrest, Impairs Cancer Cell Proliferation, Altering Glycolysis, and the TCA Cycle in Colon Cancer(Springer, 12/01/2023) Esra BULUT ATALAY; ŞERİF ŞENTÜRK; HÜLYA AYAR KAYALIThe isocitrate dehydrogenase (IDH), which participates in the TCA cycle, is an important key enzyme in regulating cell metabolism. The effect of the metabolic IDH enzyme on cancer pathogenesis has recently been shown in different types of cancer. However, the role of wild-type (wt) IDH1 in the development of colon cancer is still unknown. Our study investigated the role of the IDH1 enzyme in key hallmarks of colon cancer using various methods such as wound healing, cell cycle, colony formation ability, invasion, and apoptosis analysis. Furthermore, cell metabolism was investigated by pyruvate analysis, dinitrosalicylic acid, and HPLC methods. In addition, CRISPR/Cas9 tool was utilized to knockout the IDH1 gene in colon adenocarcinoma cells (SW620). Further studies were performed in two isogenic IDH1 KO clones. Our findings in both clones suggest that IDH1 KO results in G0/ G1 arrest, and reduces proliferation by approximately twofold compared to IDH1 WT cells. In addition, the invasion, migration, and colony formation abilities of IDH1 KO clones were significantly decreased accompanied by significant morphological changes. In the context of metabolism, intracellular glucose, pyruvate, αKG, and malate levels were decreased, while the intracellular citrate level was increased in IDH1 KO clones as compared to IDH1 WT cells. Our results reveal that wt IDH1 knockout leads to a decrease in the aggressive features of colon cancer cells. In conclusion, we reported that wt IDH1 has an effective role in colon cancer progression and could be a potential therapeutic target.Öğe SARS-CoV-2 TEDAVİSİNDE İMMÜN SİSTEMİN DESTEKLENMESİ(Eğitim Yayınevi, 2022) Demet BAYBAŞBu çalışma, SARS-CoV-2 enfeksiyonunun tedavisi ve önlenmesi için güncel durumda uygulanan ilaç tedavilerinin yanı sıra bağışıklık sisteminde önemli işlevleri olduğu bilinen bazı vitamin ve minerallerin etkilerini inceleyen örnek makalelerin derlemesidir. Diğer derlemelerden en önemli farkı, bir Biyokimya Bölümü Lisans öğrencisinin bilimsel makalelere olan bakışını içermesidir. Çalışmada COVID-19 salgını, vitamin ve mineraller ile ilgili genel bilgiler de mevcuttur. Ayrıca, çalışma Kasım 2021’e kadar yayınlanan makaleleri içeren en kapsamlı Türkçe derlemedir. Derlemede, önce COVID-19 enfeksiyonu ile ilgili genel bilgilerden, daha sonra vitaminlerin ve minerallerin (Zn, Fe, Se) viral enfeksiyonlar üzerindeki etkilerinden bahsedilecektir. Her bölümün içinde ilgili vitamin ve mineralin COVID-19 üzerine etkilerini içeren güncel makaleler ve sonuçların yer aldığı tablolar bulunmaktadır.Öğe Epigenetics: Beyond the genetics and Medicine(nova science publishers, 2022) Daştan, TanerGenetics cannot solely explain genetic variations in humans and disease developments. We see varying differences in phenotypes and disease susceptibility in organisms that have the same genetic make-up, e.g., monozygotic twins and cloned animals. The information carried by the genomic sequence is the blueprint, but the final product requires environmental determinants. Here comes the concept of epigenetics, as it is the framework where biochemical interactions between the genome and the environment blend. We can describe epigenetics as mechanisms that are beyond genetics, as such mechanisms alter the result of the genomic blueprint without altering the information itself, i.e., the sequence. Both epigenetics and epigenomics are trending research fields to better evaluate the genotype and the phenotype. The methylation of genetic material is a well-studied and well-known epigenetic marker.Öğe Nanophase surface arrays on poly (lactic-co-glycolic acid) upregulate neural cell functions(Ocak, 2022) Mimiroğlu, Didem; Yanik, Tulin; Ercan, BaturNerve guidance channels (NGCs) promote cell-extracellular matrix (ECM) interactions occurring within the nanoscale. However, studies focusing on the effects of nanophase topography on neural cell functions are limited, and mostly concentrated on the sub-micron level (>100 nm) surface topography. Therefore, the aim of this study was to fabricate <100 nm sized structures on poly lactic-co-glycolic acid (PLGA) films used in NGC applications to assess the effects of nanophase topography on neural cell functions. For this purpose, nanopit surface arrays were fabricated on PLGA surfaces via replica molding method. The results showed that neural cell prolif- eration increased up to 65% and c-fos protein expression increased up to 76% on PLGA surfaces having nanophase surface arrays compared to the control samples. It was observed that neural cells spread to a greater extend and formed more neurite extensions on the nanoarrayed surfaces compared to the control samples. These results were correlated with increased hydrophilicity and roughness of the nanophase PLGA surfaces, and point toward the promise of using nanoarrayed surfaces in NGC applications.Öğe biosensors(crc press taylor and francis, 2022) Daştan, TanerIt is our immense pleasure to introduce the book titled ‘Materials Development and Processing for Biomedical Applications’. This book is mainly focused on various methods of manufacturing, surface modifications, and advancements in biomedical applications for all kinds of readers. In particular, the fundamental aspects are discussed for a better understanding of the processing of various biomedical materials such as metals, ceramics, polymers, composites, etc. Besides, advancements in various fields of biomedical applications are emphasized. The book is basically focusing on five different aspects such as materials properties, development, processing, surface coatings, and future perspectives of advanced biomedical device fabrications. The development and applicationsÖğe cytokines and inflammation(nova science publishers, 2022) Daştan, TanerCytokines and Diseases will contribute to the pathogenesis, follow-up, and treatment processes of different clinical pictures and diseases in the light of current information obtained from the literature. This book aims to describe the type, effects, and kinetics of cytokine production, as well as to summarize the pathophysiology of the cytokine storm that occurs after bacterial sepsis or severe viral infection. It has been a summative review containing the most up-to-date data for academics participating in cytokine-based therapy studies, studies targeting cytokine production or effects, and clinical trials that arouse interest after the Covid-19 pandemic.Öğe DENTAL ANKSİYETE YÖNETİMİ – AROMATERAPİ(Gece Kitaplığı / Gece Publishing, ŞUBAT 2021) Candan Merve; Candan FerdaDental anksiyete, özellikle çocukların dental tedavi sırasında diş hekiminin ve ebeveynlerin zorlanmasına neden olan en yaygın faktördür. Fakat her yaştan erişkinleri de etkileyebilir. Hem diş hekimliğinde hem de tıpta, hastaları rahat bir şekilde tedavi edebilmek için hastanın anksiyetesini önlemek gerekmektedir. Hastayla empati kurma, doğru yaklaşım ve alternatif tedaviler, anksiyolitik ilaçların akıllıca kullanılması, sedasyon ve genel anestezinin yalnızca ciddi durumlarda tercih edilmesini sağlar. Hastanın anksiyetesi, diş hekimleri ve personelleri için önemli yönetim sorunlarını ortaya çıkarır ve endişeli bir hasta, daha uzun tedavi süresi ve tedavisi için daha fazla sayıda randevu gerektirirÖğe Chemistry, Biochemistry and Autoimmunity(Cambridge Scholars Publishing, 2021) Daştan, TanerMany mechanisms, molecular and cellular events, and responses are interferenced under autoimmunity. The dynamic biological system formed by the realization of the laws of the sciences of chemistry and physics is constantly in motion in maintaining metabolic activities in the body, in the fight against foreign molecules, in the formation of the immune response, and in the realization of autoimmune reactions. The formation of the immune response in living systems, the synthesis and interactions of molecules that occur during the immune response, and even the molecules that cause the immune response are all regulated with biological reactions maintained by chemical mechanisms.
