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Öğe An investigation of the probiotic properties of Lactobacillus fermentum(International Society of Academicians, 2020) Çetinkaya, Serap; Kocabay, Samet; Yenidunya, AliThe study assessed some of the probiotic characteristics of an isolate (AB4 26) of Lactobacillus fermentum. AB4 26 was isolated from a faecal sample of an infant, fed with breast milk. The results indicated that the isolate had acceptable survival rates in gastric juice both in the presence and absence of pepsin. It also displayed acceptable sensitivity rates to eleven different antibiotics. Hydrophobicity test showed that the isolate had a good capacity to adhere to xylene. It could also destroy sodium salts. AB4 26 displayed the least survival rates in bile salt. These initial findings could suggest that infant faeces and breast milk could serve as good sources of probiotic organisms.Öğe An Isolate of Bacillus clausii Appears to Possess Four Distinct Pectinolytic Activities(2021) Berber, Sevinç; Çetinkaya, SerapFor the bacterial source, Koyulhisar (Sivas, Turkey) apple orchard soil samples were used. Obtained isolates were identified at the species level by partial protein- and 16S rRNA gene sequence homology All of them were determined to be Bacillus clausii. Cultures were prepared with these isolates and after removing the cells, the proteins in the upper fluid were precipitated with the help of an organic solvent. While performing pectinase screening, it was noticed that an existing protease digested other proteins. This proteolytic activity was eliminated by increasing the incubation temperature to 55oC. Four different pectinase activities, polygalacturonase, pectin lyase, pectate lyase, and pectin methylesterase, were then demonstrated. Four protein bands corresponding to these activities visualised by SDS-PAGE were 80 kDa, 58 kDa, 46 kDa and ~ 28 kDa, respectively. Spectroscopic methods were employed for the identification of the enzymes. The smallest protein band (28 kDa) was found to be pectin methylesterase. Km and Vmax values of this enzyme were 0.4 and 217U, respectively.Öğe Bazı bitkisel fenolik asitlerin in vitro antioksidan aktivitelerinin incelenmesi(Cumhuriyet Üniversitesi, 2013) Çetinkaya, Serap; Yenidünya, Ali FazılBu çalışmada bazı bitkisel fenolik asitlerin antioksidan aktiviteleri araştırılmıştır. Bitkisel fenolik asitler Sigma-Aldrich (USA) ve Fluka (İndia) firmalarından temin edilmiş ve antioksidan çalışmalarında kullanılmıştır. Fenolik asitlerin antioksidan aktiviteleri 1,1-difenil-2-pikrilhidrazil (DPPH) serbest radikal giderim kapasitesi, Total Antioxidant Status (TAS) ve Total Oxidant Status (TOS) yöntemleri kullanılarak belirlenmiştir. DPPH serbest radikal giderim kapasitesinin belirlenmesinde Askorbik asit ( C vitamini) kontrol olarak kullanılarak kıyaslama yapılmıştır. Kontrol olarak kullanılan C vitamini 0,1 mg/ml de % 78,9; 0,5 mg/ml de ise % 97,7 olarak tespit edilmiştir. Buna göre çalışmada kullandığımız fitokimyasallardan Ethyl 3,4 dihydroxybenzoate? nin 0,1 mg/ml? lik konsantrasyonda % 95,5; Gallik asitte % 94,4; Rosmarinik asitte % 84,7 ve 3,5 Dimethoxy-4-hydroxycinnamic asitte % 82,35 olarak belirlenmiştir. 0,5 mg/ml? lik konsantrasyonda ise Gallik asitte % 96,94; Kafeik asitte % 96,93; 3,5 Dimethoxy-4-hydroxycinnamic asitte % 96,45 ve Ethyl 3,4 dihydroxybenzoate de ise % 95,53 olarak tespit edilmiştir. TAS analiz yönteminde elde edilen veriler trolox olarak adlandırılan E vitamini analoğuyla karşılaştırılmıştır. Buna göre, örneklerin TAS değerleri 2 mmol/L konsantrasyondan yüksek ise antioksidan kapasitesi fazladır. Çalışmada kullandığımız fitokimyasallardan 3,5 Dimethoxy-4-hydroxycinnamic asit? in 4,28 mmol/L konsantrasyon ile en fazla antioksidan seviyesine sahip olduğu tespit edilmiştir. Linoleik asit 0,03 mmol/L konsantrasyon değeriyle en düşük antioksidan aktiviteye sahip olduğu belirlenmiştir. TOS test sisteminde elde edilen veriler ticari olarak sağlanan hidrojen peroksit (H2O2) ile kıyaslanmıştır. TOS değeri 0,005 µmol/ml konsantrasyondan küçük ise antioksidan değeri oldukça yüksektir. Araştırdığımız fenollik asitlerin hepsinin değeri 0.005 µmol/ml konsantrasyondan küçük olduğu tespit edilmiştir. TOS verilerine göre en yüksek antioksidan aktiviteyi 0,0023 µmol/ml konsantrasyon değeri ile Linoleik asit? in gösterdiği tespit edilmiştir. TAS ve TOS değerleri arasındaki korelasyon Oksidatif Stres İndeksi (OSİ) ile hesaplanmıştır.Öğe Benzoat esteri içeren kumarin yapılı bileşiğin deneysel ve kuantum kimyasal hesaplamarı(2020) Saraç, Kamuran; Çetinkaya, SerapÇalışmanın amacı 4-Kumarinil-4-florobenzoatı sentezleyerek deneysel ve teorik özelliklerini tespit etmekti. 4- Kumarinil-4-florobenzoat, aroil bileşiklerinin nükleofilik katılma-ayırma reaksiyonu kullanılarak sentezlendi. Bu bağlamda 4-kumarinil 4-florobenzoat bileşiği, kuantum kimyasal hesaplamalar ve spektral teknikler kullanılarak hem deneysel hem de teorik olarak karakterize edilmiştir. Bileşiğin temel halde 1H ve 13C’ün nükleer manyetik rezonansları ve infrared spektroskopik değerleri hem deneysel olarak hem de teorik olarak hesaplandı (teorik hesaplamalar yapılırken yoğunluk fonksiyonel teorisi metodu kullanıldı). Hesaplanan infrared ve nükleer manyetik rezonan değerlerinin deneysel değerler ile uyumlu olduğu görüldü. Bileşiğin moleküler geometrisi, geometrik yapısı ve geometrik parametreler gibi kuantum kimyasal hesaplamarı 6-311G(d,p) temel seti ile hesaplandı. HOMO-LUMO arasındaki enerji farkı, kimyasal sertlik ve kimyasal yumuşaklık gibi elektronik özelliklerin kuantum kimyasal hesaplamarı yapıldı. 4-Kumarinil-4-florobenzoat‘ın moleküler elektrostatik potansiyel (MEP) yüzeyi elde edildi.Anahtar kelimeler: DFT, kumarin, HOM-LUMO, moleküler modelleme.Öğe Biyoaktif molekül analoglarının yapımında kullanılabilir şeker esterlerinin sentezi(Cumhuriyet Üniversitesi, 2018) Çetinkaya, Serap; Yenidünya, Ali FazılŞeker-yağ asidi esterlerinin sentezinde kısıtlayıcı parametre organik ortamda substrat çözünürlüğüdür. Şekerler birçok organik ortamda yeterince çözünmemektedir. Öte yandan şekeri çözen birçok organik ortam enzim aktivitesine elverişli değildir. Ayrıca bu iki temel koşulu karşılayan organik çözücülerin çoğu tepkime ortamında birbiri ile faz oluşturabilmektedir. Bu üç sorunu bertaraf edebilmek için ilk çalışmalar çözünürlük kapsamında yürütüldü. Bulgular doğrultusunda, tepkime ortamı olarak iki organik çözücü çifti tercih edildi: dimetilsulfoksit/tert-bütanol ve dimetil sülfoksit/2-metil-2-bütanol. Dimetilsulfoksit yerine dimetilformamit de kullanılabilirdi. Ancak, şeker çözünürlüğünün dimetilformamitde nispeten daha az olduğu saptandı. Her bir şekerin esterleşmede farklı davranış gösterebileceği düşüncesiyle birden fazla şeker denendi. Örneğin, ribozların doğada fonksiyonel moleküllerde yapı birimi olarak heksozlardan çok daha yaygın tercih edilmesine karşın, mevcut literatürde şeker esterlerinde hiç kullanılmadığı görüldü. Yağ asidi zincir uzunluğunun tepkime verimi üzerinde etkili olduğuna ilişkin bilgi vardır. Bu nedenle deneylerde birden fazla yağ asidi kullanıldı.Şeker esterleri sırasıyla ince tabaka kromatografisi, IR, ve NMR ile analiz edildi. Ayrıca yalnızca bir örneğin HSQC ve kütle spektrometri analizi de yapıldı.Kullanılan şeker ve yağ asidinin cinsinden bağımsız olarak enzim içermeyen kontrol deneyleri de, her seferinde esterleşme ürünü verdiğinden, diğer örneklere uygulanan işlemler ve analiz yöntemlerine bu örnekler de dahil edildi. Rasgele örnekler seçilerek HPLC ile ppm düzeyinde verim analizi yapıldı. Elde edilen bulgular organik bir tepkime ortamında ve enzim ya da tanımlı bir kimyasal katalizör yokluğunda şeker esterlerinin sentezlenebildiğini tekrarlı olarak doğruladı. Bu sonuç literatürde mevcut olmayıp, teze özgü orijinal bir bulgudur. Bu bulgu yine literatürde mevcut olmayan ve farklı yağ asitleri ile sentezlenen riboz esterleri için de doğrulanmıştır.Öğe Effective removal of methylene blue dye from aqueous solution using Macrolepiota procera mushroom: Experimental and theoretical studies(Elsevier B.V., 2025) Eyupoglu, Volkan; Akin, Muhammed Bora; Kaya, Savaş; Çaylak, Osman; Berisha, Avni; Çetinkaya, SerapThis study investigated Macrolepiota procera mushroom biomass as a biosorbent for removing methylene blue (MB) dye from aqueous solutions. Key adsorption parameters such as pH, biosorbent dosage, and contact time were optimized, achieving a maximum adsorption capacity of 1.404 mol·kg−1 at pH 9, with 100 mg biosorbent and a temperature of 25 °C. SEM, EDX, and FT-IR analyses characterized the biosorbent's surface morphology and functional groups. Adsorption followed the Langmuir isotherm model, showing high affinity in alkaline conditions, and efficiency increased by 90.88 % with 200 mg biosorbent. Kinetic data fit Pseudo-Second and Pseudo-First Order models, and thermodynamics indicated an endothermic, spontaneous process. Recovery tests revealed ∼ 4 % retained activity after five cycles. Density Functional Theory calculations supported experimental adsorption energies, confirming chitin's role in MB binding. © 2024 Elsevier B.V.Öğe Effects of Detergents, Ions, and Organic Solvents on the Activity of Four Bacillus clausii Pectinases(2020) Berber, Sevinç; Çetinkaya, SerapFour different pectinolytic enzyme activity essays were employed to detect different pectinases ofBacillus clausii from an extracellular protein cocktail. The mixture was obtained by ethanol precipitation.Dinitrosalicylic acid (DNS) and sodium hydroxide (NaOH) titrimetric methods were used for thepectinase assays. Each of the essays produced a positive result, indicating the presence of pectate lyase(PGL), pectin lyase (PL), pectin methyl esterase (PME), and polygalacturonase (PG). Activities of theseenzymes were then assessed at differing concentrations of NaCl, detergents (SDS and tweens), ionchelators, and organic solvents. Results, presented as histograms, were the indication of original findings,as most of them were new to the relevant literature.Öğe GENETIC INTERPLAY BETWEEN THE DAIRY STREPTOCOCCUS THERMOPHILUS AND ITS PHAGES(İksad publishing house, 2021) Çetinkaya, Serap; Yenidünya, Ali FazılThe chapter was prepared with the intention to provide a concise information on the genetics of dairy S. thermophilus in relation to its phages. The text was extricated from key references with relevant Figures. In essence, it was tried to make a collection of the key findings on the subject and to reemphasize them together.Öğe GENETIC INTERPLAY BETWEEN THE DAIRY STREPTOCOCCUS THERMOPHILUS AND ITS PHAGES(İksad publishing house, Ağustos 2021) Çetinkaya, Serap; Yenidünya, Ali FazılThe chapter was prepared with the intention to provide a concise information on the genetics of dairy S. thermophilus in relation to its phages. The text was extricated from key references with relevant Figures. In essence, it was tried to make a collection of the key findings on the subject and to reemphasize them together.Öğe Isolation of Traditional Yogurt Yeast Kluyveromyces marxianus and Investigation of Major Probiotic Properties(Sivas Cumhuriyet Üniversitesi, 2025) Çetinkaya, SerapThe aim of this study was to evaluate the probiotic potential of Kluyveromyces marxianus K3 yeast strain isolated from cow yogurt. Kluyveromyces marxianus yeast strain was isolated from yogurt and identified based on ITS sequences. The isolated strain showed high tolerance to low pH conditions. This feature can be associated with the ability of the strain to survive in acidic environments such as stomach acid. In addition, the strain showed tolerance to simulated human gastric and intestinal fluids, indicating that it can move healthily in the digestive system. It was determined that the isolate was resistant to antibiotics, indicating its potential to help protect the intestinal flora. It was determined that the strain grew well at human body temperature, exhibited hydrophobic properties and had deconjugation ability against bile salts. The research findings indicate that Kluyveromyces marxianus strain obtained from yogurt has the potential to be used as a probiotic in different food products. This species is an important candidate that can be included in food supplements or new probiotic formulations. In conclusion, this study reveals that yogurt is a rich source of probiotic yeast species and Kluyveromyces marxianus K3 strain may play an important role in this fieldÖğe Modification by natural sources to reduce immuno-reactivity of milk proteins(2020) Akkaya, Recep; Akkaya, Birnur; Çetinkaya, SerapThe main aim of the current study was to reduce the IgE-binding capacity of cow’s milkthrough its chemical modification by natural source treatment. The presence of childrenallergic responses to cow's milk has become a growing concern in the world. A possibleapproach to reduce protein allergen is to block IgE-binding epitopes of protein allergen byvarious methods. One of them is protein glycation. We wanted to examine effect of someadditives especially lemon juices on milk protein modification by using electrophoresis and2D gel electrophoresis. As a result of this study lemon juice (ascorbic acid) enhanced glycationof milk proteins.Öğe Novel imidazo[2,1-b] thiazole-based anticancer agents as potential focal adhesion kinase inhibitors: Synthesis, in silico and in vitro evaluation(Wiley Online Library, 2021) Başoğlu, Faika; Ulusoy-Güzeldemirci, Nuray; Akalın-Çiftçi, Gülşen; Çetinkaya, Serap; Ece, AbdulilahThe purpose of this study was to synthesize imidazo[2,1-b] thiazole derivatives, characterize them with spectroscopical techniques and investigate for cytotoxic and apoptotic effects on glioma C6 cancer cell line. The in vitro anticancer activities were also investigated against focal adhesion kinase. Most of the compounds, particularly the derivatives carrying 3-oxo- 1- tiya- 4- azaspiro[ 4.5]decane moiety, exhibited higher or comparable activities in comparison with the reference drug, cisplatin. Compounds with methyl, propyl, phenyl moieties at the eighth and second position of the spirothiazolidinone ring showed high FAK inhibitory activities. In addition, molecular docking studies shed light on the binding modes of the synthesized compounds. The critical interactions with amino acid residues located in the active site were revealed. The results obtained from both biological assay data and computational results might provide insight into developing new inhibitors against focal adhesion kinase.Öğe A Novel Isolate (S15) of Streptomyces griseobrunneus Produces 1?Dodecanol(Springer, 2021) Çetinkaya, SerapOne-dodecanol was identified to be the predominant secondary metabolite of a novel isolate (S15) of Streptomyces griseobrunneus. For its demonstration, secondary metabolite extracts were electrophoresed by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE). A yellowish unique band was then cut out from the gel and its metabolite content was eluted in n-butanol. GC–MS analysis indicated that more than 93% of the of the elution material were 1-dodecanol. The compound was further characterized by FTIR and 13C NMR analyses. Dendrogram built on the basis of 16S rRNA gene sequence indicated that the isolate S15 was a member of Streptomyces griseobrunneus.Öğe Purification and characterization of glucoamylase from Bacillus sp. isolated from root flora of Prunus mahaleb tree by LC-MS/MS analysis(Elsevier B.V., 2025) Çelik, Muhammed Safa; Kapancık, Serkan; Seyran, Esra; Çetinkaya, SerapGlucoamylases are enzymes that release free glucose by hydrolyzing consecutive α-1,4 bonds at the non-reducing ends of starch molecules. This enzyme was purified using ammonium sulfate precipitation, and its molecular mass was determined to be approximately 65.2 kDa via SDS-PAGE. Using zymogram analysis, the purified sample's active glucoamylase content was verified. Nano-Liquid Chromatography Mass Spectrometry (nLC-MS/MS) characterization identified peptides covering 46 % of the glucoamylase protein sequence, indicating partial characterization of the enzyme. It was found that the ideal pH and temperature for glucoamylase activity were 6.0 and 37 °C, respectively. Using soluble starch as a substrate, the kinetic parameters were calculated: the Km (substrate concentration at half-maximal velocity) was 30.21 μM, and the Vmax (maximum reaction velocity) was 35.59 μmol mg protein−1 min−1. The enzyme demonstrated optimal activity with soluble starch, highlighting its specificity for starch hydrolysis. Additionally, the enzymatic activity was enhanced in the presence of CaCl2, indicating a positive effect of calcium ions. Its optimal conditions and kinetic parameters provide valuable insights for its industrial and biomedical use. © 2025 Elsevier B.V.Öğe Studies on pyrimidine derivatives(Nova Science Publishers, Inc., 2024) Çetinkaya, Hüseyin Fatih; Çelik, Muhammed Safa; Abbaszada, Nübar; Çetinkaya, Serap; Tüzün, BurakPyrimidine is a nitrogen-containing heterocyclic aromatic compound. Together with its derivatives it plays an expansive role in drug discovery studies. In the chemistry of biological systems, pyrimidine derivatives have engrossed interests as they formed the bases of therapeutic natural products. They are the building blocks of many natural compounds: antibiotics, liposaccharides, and vitamins, to name a few. Pyrimidine is used in heterocyclic drugs with antimicrobial, anti-inflammatory, antidiabetic, antiviral, anticancer, and antifungal activities. Hence, it also serves as a versatile tool in the theoretical development of heterocyclic chemistry and organic synthesis. This study attempted to cover various pyrimidine derivatives with powerful biological and pharmacological applications. © 2024 Nova Science Publishers, Inc. All rights reserved.Öğe The effects of aspirin acetylation of human serum albumin on its interactions with methotrexate(Elsevier B.V., 2025) Seyran, Esra; Çetinkaya, SerapHuman serum albumin (HSA) is the most abundant protein in the blood and serves as the primary carrier protein. HSA transports a wide variety of pharmaceuticals and other compounds, influencing the bioavailability of its binding partners. For example, HSA binds to and is acetylated by aspirin. While the acetylation of HSA by aspirin is a well-known reaction, its role in regulating HSA's carrier function has not been thoroughly explored. This study examined the effects of aspirin acetylation on HSA and its interactions with methotrexate in vitro. The acetylation sites on HSA were mapped using mass spectrometry. The results revealed that the pattern of aspirin acetylation of HSA is time-dependent and that aspirin preferentially acetylates lysine residues in both of HSA's principal drug-binding sites. Additionally, aspirin and another pharmaceutical, methotrexate, competed for binding to site 1, as methotrexate inhibited the aspirin-induced acetylation of HSA. Importantly, the results indicated that aspirin acetylation of HSA compromised HSA's ability to bind to methotrexate. Overall this interaction has the potential to modulate the drug binding dynamics of HSA. Further research is needed to determine how the competitive inhibition of aspirin-induced acetylation might influence the pharmacokinetic and pharmacodynamic factors in clinical settings. © 2024 Elsevier B.V.
