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Article Citation - Scopus: 1An Investigation on the Dna Binding Activities of Melamine, Cyanuric Acid and Uric Acid(Editura Acad Romane, 2021) Senol, Ali; Devrim, Alparslan Kadir; Sudagidan, Mert; Ozalp, Veli CengizMelamine can be added to various foods such as milk, milk powder, baby food, pet, and livestock feed for cheating purposes due to its high nitrogen content. Regarding its usage in food products, there is a need to investigate its possible interactions with DNA. Thus, this study aimed to investigate the interactions of melamine and its metabolized products, cyanuric acid and uric acid with genomic DNA, isolated from eukaryotic (calf thymus) and prokaryotic (Staphylococcus aureus) sources. UV-absorbance spectrophotometry, fluorescence spectrophotometry, and agarose gel electrophoresis techniques were used to evaluate these interactions. The five different concentrations of melamine, cyanuric acid, and uric acid were incubated with fixed DNA concentration and it was determined that the test compounds interacted with the DNA molecules. The data obtained by UV-absorbance and fluorescence spectrophotometry techniques revealed an increase in wave peaks observed with the increasing substance concentration. After the obtained data of the aforementioned techniques were evaluated together, it was concluded that melamine, cyanuric acid, and uric acid bonded to the eukaryotic and prokaryotic genomic DNA materials via groove binding.Article Citation - WoS: 19Citation - Scopus: 19Metagenomic and Chemical Analysis of Tarhana During Traditional Fermentation Process(Elsevier, 2021) Soyucok, Ali; Yurt, Mediha Nur Zafer; Altunbas, Osman; Ozalp, Veli Cengiz; Sudagidan, MertTarhana is one of the favourable traditional fermented food consumed as a soup. Different flour, vegetables, spices and yogurt are main constituents and they compose of microbiota of Tarhana. In this study, bacterial communities in each fermentation process and in their constituents were identified by metagenomic analysis. Also, chemical properties (pH, acidity, salt content and dry matter) were analysed in each step. The results showed that in the dough formation, mainly Lactobacillus, Bacillus, Enterococcus and Streptococcus were present and after Day 4, Clostridium and Bacillus became dominant, after drying Clostridium disappeared and in the final product bacterial communities from Bacillus and Streptococcus genus were observed. Chemical analysis showed that pH decreased from 4.94 to 4.46, acidity increased by time at the beginning of fermentation from 7.5% to 22.5% in first 6 days period, then, became stable at 14% in drying process. Salt content increased by time from 1.74 to 3.08 g salt/100 g Tarhana in first 8 days and in drying process salt content was recorded as 2.81-2.90 and dry matter was obtained as 94 g dry matter/100 g Tarhana in the final product. This study elucidated the effects of ingredients, raw materials and how microbiota and chemical properties changes during fermentation steps of home-made traditional Tarhana production and thus preparation methods could be developed to obtain standardized Tarhana products for industrial production in future.Article Citation - WoS: 8Citation - Scopus: 8Surface Microbiota and Associated Staphylococci of Houseflies (musca Domestica) Collected From Different Environmental Sources(Academic Press Ltd- Elsevier Science Ltd, 2022) Sudagidan, Mert; Ozalp, Veli Cengiz; Can, Ozge; Eligul, Hakan; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Kocak, OnerHouseflies (Musca domestica) are important mechanical vectors for the transmission of pathogenic microorganisms. In this study, 129 houseflies (69 males and 60 females) were collected from 10 different environmental sources and a laboratory population was used. The surface microbiota of houseflies was identified by NextGeneration Sequencing. Staphylococci from the surfaces of houseflies were selectively isolated and their virulence genes, antibiotic susceptibilities, biofilm formation, and clonal relatedness were determined. Metagenomic analysis results demonstrated that Staphylococcus, Bacillus, and Enterococcus were mostly present on the surface of houseflies at the genus level. Additionally, the isolated 32 staphylococcal strains were identified as Staphylococcus sciuri (n = 11), S. saprophyticus (n = 9), S. arlettae (n = 6), S. xylosus (n = 4), S. epidermidis (n = 1) and S. gallinarum (n = 1). tetK, tetM, tetL, ermC, msrAB, and aad6 genes were found to carry by some of the staphylococcal strains. The strains were mostly resistant to oxacillin, penicillin, and erythromycin and three strains were multi-drug resistant. There was a statistical difference between housefly collection places and antibiotic resistance of isolated staphylococci to penicillin G, gentamicin, and erythromycin (p < 0.05). Biofilm test showed that 17 strains were strong biofilm formers, and it plays important role in the transmission of these bacteria on the surface of houseflies. Staphylococcal strains showed extracellular proteolytic and lipolytic activity in 31 and 12 strains, respectively. Closely related species were found in PFGE analysis from different environmental sources. By this study, surface microbiota and carriage of pathogenic staphylococci on the surfaces of houseflies and their virulence properties were elucidated.Article Enhancement of Paclitaxel Therapeutic Effect by Aptamer Targeted Delivery in Plga Nanoparticles(2021) Dursun, Ali; Dursun, Ali Doğan; Ucak, Samet; Özalp, Veli Cengiz; Poyraz, Fatma Sayan; Yilmaz, Elif; Mansuroglu, Banu; Ozalp, Veli Cengiz; Dursun, Ali Doğan; Özalp, Veli Cengiz; Basic Sciences; Basic SciencesObjectives: Paclitaxel is a drug molecule used in the therapy of various cancer types, including breast cancer. It is one of the preferred chemotherapy agent due to its high efficacy. However, many side effects have been observed associ- ated with paclitaxel use such as allergy, hair loss, diarrhea and pain. Methods: We evaluated therapeutic efficacy of paclitaxel when it is actively targeted to breast cancer tumours inside a polymeric nanoparticle. Targeted delivery of paclitaxel to tumour sites has been reported as an improved cytotoxicity strategy with a variety of nanoparticles. In this study, poly Lactic-co-Glycolic Acid (PLGA) nanoparticles were used as drug carrier and nucleolin aptamers as affinity targeting agents. Results: Paclitaxel molecules were entrapped during the synthesis of PLGA nanoparticles of 238 nm in diameter. The encapsulation and loading efficiencies of paclitaxel was 97% and 21% respectively. The paclitaxel loaded PLGA nanoparticles were functionalized with nucleolin aptamers and their targeting ability to cultured mouse cancer cells was determined for two cell lines (E0771 and 4T1). E0771 cell line was chosen for the preparation of allograph breast cancer mouse models. Evaluations of the targeted paclitaxel in PLGA nanoparticles showed 38% better performance in inhibiting tumour growth compared to free paclitaxel treatment groups of mouse models. Conclusion: The chemotherapeutic effect of cancer drugs like paclitaxel can be increased by loading inside tumour targeted polymeric nanoparticlesArticle Citation - WoS: 7Citation - Scopus: 8Aptamer-Based Magnetic Isolation and Specific Detection System for listeria Monocytogenes from Food Samples(Elsevier, 2024) Bayramoglu, Gulay; Ozalp, Veli Cengiz; Arica, Mehmet YakupIn this work, an aptamer-based magnetic system was designed for specific and rapid detection of Listeria monocytogenes in food samples. To prepare the selective magnetic system against the target bacterium, firstly, magnetic particles (Fe3O4) were coated with two hydrophilic polymer layers. The specific aptamer immobilized magnetic system efficiently captured L. monocytogenes cells in a competitive response time of approximately 10 min. The magnetic aptamer detection system was very specific to L. monocytogenes and had high selective, up to 97.6 % compared to the Listeria species (Listeria ivanovii, Listeria innocua, and Listeria seeligeri) and other bacteria species Escherichia coli, Staphylococcus aureus, and Basillus subtilus. The isolation and detection of L. monocytogenes from food samples using the presented method are fast and reliable. Moreover, another significant factor to be contemplated is the use of a few chemicals for detection, reducing the cost of analysis, and the results can be obtained within 18 h.Article Citation - WoS: 17Citation - Scopus: 19Bacterial Surface, Biofilm and Virulence Properties of listeriamonocytogenes Strains Isolated From Smoked Salmon and Fish Food Contact Surfaces(Elsevier, 2021) Sudagidan, Mert; Ozalp, Veli Cengiz; Ozturk, Orhan; Yurt, Mediha Nur Zafer; Yavuz, Orhan; Tasbasi, Behiye Busra; Aydin, AliBiofilm formation is one of the defense mechanisms of bacteria against disinfectants and antimicrobials. The aim of this study was to determine biofilm-forming L.monocytogenes from fish processing and salmon surfaces. Biofilm formation at 15, 25, 37, and 40 degrees C from 1 to 6-days period, adhesion to glass, polypropylene and stainless-steel surfaces, bacterial surface charge and hydrophobicity was determined. Adhesion behavior of the strains was evaluated using Surface Plasmon Resonance (SPR) technique. Totally 32 L.monocytogenes strains belonging to serogroups IIa (n:17), IIc(n:14) and IVb(n:1) were detected from 1320 swabs and 16 smoked salmons. Biofilm formation tests revealed that 21 strains form biofilm on microplate by increasing time and temperature. Although all strains strongly formed biofilm on glass surfaces, two strains slightly adhered polypropylene surfaces. High surface roughness of stainless-steel FeCrNi alloy (Ra = 4.15 nm) and CoCrMo alloy (Ra = 10.75 nm) increased biofilm formation of L.monocytogenes on stainless-steel surfaces. Zeta potential results showed that non-biofilm formers were more negatively charged after 6-days and hydrophobicity couldn't give a distinct distribution among biofilm formers and non-formers. SPR analysis method was evaluated to distinguish biofilm formers to adhere SPR gold chip surfaces. PCR results revealed that all strains were positive for hylA, iap, actA, plcA, plcB, fri, flaA, inlA, inlB, inlC, inlJ, and lmo1386 genes. Additionally, all strains were susceptible to penicillin, ampicillin, meropenem, erythromycin and trimethoprim-sulfamethoxazole. Biofilm-forming, virulence properties of L. monocytogenes strains isolated from fish processing surfaces and smoked salmons were evaluated and SPR was used to differentiate biofilm formers as a sensitive technique for biofilm studies.Article Citation - Scopus: 2The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain(Mdpi, 2023) Ersoy Omeroglu, Esra; Bayer, Asli; Sudagidan, Mert; Ozalp, Veli Cengiz; Yasa, IhsanAccess to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.Article Selection of DNA Aptamers Against Parathyroid Hormone for Electrochemical Impedimetric Biosensor System Development(John Wiley and Sons Inc, 2025) Didarian, Reza; Bargh, Saharnaz; Gulerman, Almina; Ozalp, Veli Cengiz; Erel, Ozcan; Yildirim-Tirgil, NimetThis work presents the pioneering development of an aptamer-based electrochemical biosensor for real-time monitoring of parathyroid hormone (PTH) levels, with a focus on intraoperative assessment during parathyroid surgery. It introduces, for the first time, the selection and characterization of aptamers targeting distinct segments of the PTH peptide. The study demonstrates the feasibility and efficacy of the biosensing platform through a precisely designed experimental framework, including SELEX-based aptamer selection, aptamer-peptide interaction analysis, and biosensor fabrication. The SELEX process yields aptamers with notable binding affinities to different fragments of PTH, with the PTH (53-84) aptamer showing particularly sensitive binding to the hormone's C terminus, allowing for precise PTH analysis. Electrochemical characterization reveals significant changes in electrochemical impedance spectroscopy (EIS) signals upon exposure to varying PTH concentrations, highlighting the sensor's sensitivity and selectivity. The increase in charge transfer resistance (Rct) values with rising PTH concentrations underscores the biosensor's capability to detect PTH-induced structural changes, validating its potential for accurate measurement. The biosensor shows remarkable selectivity in the presence of common interferents in serum samples, ensuring precise PTH detection. Stability assessments over a 45-day storage period demonstrate the biosensor's robustness and long-term reliability, affirming its practical suitability. In summary, the developed aptamer-based biosensor represents a promising tool for sensitive and selective PTH detection, with potential applications in biomedical research and clinical diagnostics, particularly for intraoperative PTH analysis during parathyroidectomy. Continued research and optimization efforts hold promise for enhancing its performance and expanding its utility in diverse healthcare settings.Article Citation - WoS: 3Citation - Scopus: 3Paper-Based Aptasensor Assay for Detection of Food Adulterant Sildenafil(Mdpi, 2024) Kavruk, Murat; Ozalp, Veli CengizSildenafil is used to treat erectile dysfunction and pulmonary arterial hypertension but is often illicitly added to energy drinks and chocolates. This study introduces a lateral flow strip test using aptamers specific to sildenafil for detecting its illegal presence in food. The process involved using graphene oxide SELEX to identify high-affinity aptamers, which were then converted into molecular gate structures on mesoporous silica nanoparticles, creating a unique signaling system. This system was integrated into lateral flow chromatography strips and tested on buffers and chocolate samples containing sildenafil. The method simplifies the lateral flow assay (LFA) for small molecules and provides a tool for signal amplification. The detection limit for these strips was found to be 68.2 nM (31.8 mu g/kg) in spiked food samples.Article Citation - WoS: 24Citation - Scopus: 30High-Efficiency Application of Cts-Co Nps Mimicking Peroxidase Enzyme on Tmb(ox)(Pergamon-elsevier Science Ltd, 2022) Altuner, Elif Esra; Ozalp, Veli Cengiz; Yilmaz, M. Deniz; Bekmezci, Muhammed; Sen, FatihIn this study, analytical studies of Chitosan-Cobalt(II) (CTS-Co(II)) nanoparticles (CTS - Co NPs) by mimicking horseradish peroxidase (HRP) were evaluated. In the applications, it was observed that CTS-Co NPs 3,3 ' 5,5 ' tetramethylbenzidine (TMB) oxidized in the presence of hydrogen peroxide (H2O2). The required CTS-Co NPs were synthesized at 50 degrees C in 30 min and characterized using Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), inductively coupled plasma-optical emission spectroscopy (ICP-OES), and Xray photon spectroscopy (XPS) was done. CTS-Co NPs were studied to develop a selective TMB biosensor on TMB (ox) substrate. The synthesized CTS-Co NPs formed a catalytic reaction with 30% 0.2 mM H2O2 on 0.2 M TMB substrate. After the catalytic reaction, sensitive signals were obtained from the desired biosensor. Electrochemical measurements were taken as low limit of 10 mg and a high limit of 20 mg for the determination of CTSCo NPs to TMB(ox). In the microplate study; The sensors were applied on 1.5 mu g and 3 mu g CTS-Co NPs TMB(ox) substrate, respectively. CTS- Co NPs; for TMB(ox) determination, optical density (OD) measurement was taken as a low limit of 1.5 mu g and a high limit of 3 mu g. Electrochemical applications of particles and microplate reader results were compared with horseradish peroxidase (HRP) enzyme for sensor properties. According to the data obtained, it was observed that it behaved similarly to the CTS-Co NPs peroxidase enzyme. This work presents innovations for nanoparticle extraction and sensor study from chitosan and other naturally sourced polymers.
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