Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 1Citation - Scopus: 1The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots(Wiley, 2024) Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.imageArticle Citation - WoS: 9Citation - Scopus: 8Quantitative Determination of Phenolic Compounds in Propolis Samples From the Black Sea Region (türkiye) Based on Hptlc Images Using Partial Least Squares and Genetic Inverse Least Squares Methods(Elsevier, 2023) Güzelmeriç, Etil; Özdemir, Durmuş; Şen, Nisa Beril; Çelik, Cansel; Yeşilada, ErdemThe complex chemical composition of propolis is related to the plant source to be used by honeybees. Propolis type is defined based on the plant source with the highest proportion in its composition, which is determined by chromatographic techniques as high-performance thin-layer chromatography (HPTLC). In addition to marker component identification to specify the propolis type, quantification of its proportion is also significant for prediction and reproducible pharmacological activity. One drawback for propolis marker component quantita-tion is that during the chromatographical analysis, not the main but the other plant sources with less proportion may cause interferences during the chemical analysis. In this study, the amounts of marker components were compared with the reference analysis data obtained by high-performance liquid chromatography (HPLC) and from HPTLC images using Partial Least Squares (PLS) and Genetic Inverse Least Squares (GILS) regression methods. Firstly, HPTLC images of propolis samples were processed by an image algorithm (developed in MATLAB) where the bands of each standard and the samples were cut same dimensional pieces as 351 x 26 pixels in height and width, respectively. Simultaneously, reference analysis of the marker components in propolis samples was performed with a validated HPLC method. Consequently, the reference values obtained from HPLC versus PLS, and GILS predicted values of the eight compounds based on the digitized HPTLC images of the chromatograms were found to be matched successfully. The results of the multivariate calibration models demonstrated that HPTLC images could be used quantitatively for quality control of propolis used as a food supplement.Article Citation - WoS: 7Citation - Scopus: 6Visceral Leishmaniasis Caused by Leishmania Tropica(Springer, 2023) Özbilgin, Ahmet; Tunalı, Varol; Çavuş, İbrahim; Vardarlı Tetik, Aslı; Dinç, Melike; Yalçın, Talat; Gündüz, Cumhur; Beyaz, Merve; Köse, ŞükranPurposeIn Turkey, the main causative agent of visceral leishmaniasis (VL) is Leishmania. infantum and the main causative agent of cutaneous leishmaniasis (CL) is Leishmania tropica. In this study, we aimed to discuss the possible mechanisms, clinical aspects, and threat of visceralizing L. tropica.MethodsThis study includes seven cases of VL caused by L. tropica.Five patients were male (71%) and four were adults (57%).ResultsAll the VL patients complained of fever and splenomegaly. Fatigue, pancytopenia, and hepatomegaly were present in six patients each (86%), while weight loss and gastrointestinal system (GIS) symptoms were present in 5 patients (71%).ConclusionsIn this study, we have evaluated seven cases of visceralized L. tropica (VLT) in the context of the changing leishmaniasis epidemiology in Turkey. We have evaluated the possible mechanisms of visceralization; inter- and intraspecies genetic exchange with all the old world leishmaniasis agents present in the region, stress induced by inappropriate use of drugs, and possible ongoing adaptation mechanisms of Leishmania spp. The threat posed by VLT is significant as L. tropica is the most widespread and most common cause of leishmaniasis in Turkey. We do not know the vectorial capacity of the sand flies for the transmission of VLT strains or if these strains are in circulation in Turkey. Future studies should be carried out to investigate these issues as the transition of L. tropica from a mild disease-causing agent to a mortal one poses a significant public health concern for Turkey and Europe.Article Citation - WoS: 2Citation - Scopus: 4Identification of Turkish Extra Virgin Olive Oils Produced in Different Regions by Using Nmr (h-1 and C-13) and Irms (c-13/C-12)(Wiley, 2023) Sevim, Didar; Köseoğlu, Oya; Ertaş, Hasan; Özdemir, Durmuş; Ulaş, Mehmet; Günnaz, Salih; Çelenk, Veysel UmutIsotope ratio mass spectroscopy (IRMS) and nuclear magnetic resonance (NMR) spectroscopy techniques are two of the analytical methods that are used to characterize food products. The aim of this study is to classify extra virgin olive oil (EVOO) samples collected from different regions of Turkey based on H-1 and C-13 NMR spectra along with IRMS d(13)C carbon isotope ratio data by using chemometrics multivariate data analysis methods. A total of 175 EVOO samples were analyzed in 2014/15 and 2015/16 harvest seasons. Multivariate classification and clustering models were used to identify geographical and botanical origins of the EVOOs. IRMS results showed that there was no significant difference in terms of d(13)C values between the years in terms of harvest year (p > 0.05), only extraction phase and variety were statistically significant factors (p < 0.05). The interactions of the factors showed that the harvest year x variety interaction is important. The outcomes of this research clearly indicated that considering the partial least squares discriminant analysis result with NMR spectra, the percent success of the model in the South Marmara, North Aegean, and South Aegean region samples were 95%, 95.7%, and 96.4% in the model set, respectively. The results showed that by using classification and clustering models, geographic marking and labeling of these oils can be carried out regardless of differences in year and production systems (2 and 3 phase extraction system) according the NMR analysis.Article Citation - WoS: 3Citation - Scopus: 3Synthesis and Antifungal and Antibacterial Bioactivities of Diborolanes Containing Arylamines(Elsevier, 2023) Aygün, Muhittin; Sevinçek, Resul; Özgener, Hüseyin; Bıyık, Hacı Halil; Metin, Kubilay; Şahin, Yüksel; Poyrazoğlu Çoban, Esra; Gürbüz, BurçinA good yield of 1,2-diarylamino-1,2-diborolanes 2 was obtained from the reaction of 1,2-dichloro-1,2-diborolane 1 and ArNHLi (an anilide). The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2a and 2b were also determined using single-crystal X-ray diffraction. Antimicrobial activities of synthesized compounds against some Gram-positive and -negative bacteria and yeasts were determined. Some compounds were found to have strong antibacterial and antifungal properties, especially against the bacterium, S. pneumonia, which is the causative agent of pneumonia, and the fungus, C. albicans, which is the causative agent of candidiasis. The compounds 2a and 3 had a powerful effect (compound 2a and 3 = 1 μgmL−1) against S. pneumoniae ATCC 27336 bacteria. In addition, compounds 2a, 3 and 2f were observed to have strong effects (compound 2a, 3, 2f = 2 μgmL−1) against C. albicans ATCC 10231 and C. utilis ATCC 9950. The results obtained were found to be more effective than the MIC values (128–64 μgmL−1) of Streptomycin and Flukanozol drugs used for bacteria and yeasts. The results of our study show that the synthesized substances can be used for new drug applications that are being developed against infectious diseases in the pharmaceutical industry. © 2023 Elsevier B.V.Article Citation - WoS: 3Citation - Scopus: 3Continuous Production of Hyperbranched Polyhydrocarbons by Electrochemical Polymerization of Chlorinated Methanes(Royal Society of Chemistry, 2022) Seo, Jae Hong; Nam, Hyun Ju; Rajendiran, Rajmohan; Seong, Won Kyung; Jiang, Yi; Kim, Min Hyeok; Büyükçakır, OnurA continuous production of polyhydrocarbon (PHC) by electrochemical polymerization of chlorinated hydrocarbons is presented. Monomer loading and product transfer were controlled by changing flow direction in a home-built continuous flow system that facilitates preparation, work-up, and scale-up of electrochemical polymerization. The polymerization can be tuned by adjusting reaction time, cell configuration, molar ratio of input chemicals, and the solvent type. CH2Cl2, CHCl3, and CCl4 were used to synthesize PHC. The reduction of the monomers at the cathode was studied by cyclic voltammetry and chronoamperometry. We investigated the structure and composition of PHCs from FT-IR and NMR spectra along with elemental analysis. Sufficient amounts of product are generated by continuous production and characterization of the product PHCs by a wide variety of methods is possible. Particularly, structural analysis by various C-13 NMR techniques suggests a new pathway for the synthesis of hyperbranched PHCs by electrochemical polymerization.Article Citation - WoS: 10Citation - Scopus: 12Determination of the Quality and Purity Characteristics of Olive Oils Obtained From Different Regions of Turkey, Depending on Climatic Changes(Wiley, 2022) Sevim, Didar; Köseoğlu, Oya; Özdemir, Durmuş; Hakan, Mehmet; Büyükgök, Elif B.; Uslu, Hatice; Dursun, ÖzgürVirgin olive oils (VOOs) obtained from olives grown in different regions of Turkey under changing climatic conditions sometimes show different sensory and chemical properties. This study was planned to determine whether these deviations are due to climatic changes or not. For this purpose, five different olive varieties (Ayvalik, Memecik, Gemlik, Nizip Yaglik, Kilis Yaglik) of commercial importance were harvested from the provinces/districts (four different region) where cultivation is intense during the 2017/2018-2020/2021 harvest years. Every year, olive samples were collected from 3 orchards from 13 provinces/districts. One hundred and fifty-six samples were subjected to the purity, quality and sensory analysis. Basic climatic values (average, minimum and maximum temperature, humidity and precipitation) were examined for four consecutive years. All of the examined olive oil samples were determined within the legal limits in terms of fatty acid composition and fatty acid ethyl ester values. However, delta-7-stigmastenol value from the sterol composition was found to be above 0.5% in some samples in all the years studied (total 21 samples). Delta-7-stigmastenol values of olive oil samples varied between 0.16% and 1.14%. Multiple linear regression analysis was applied using a genetic algorithm-based inverse least squares method to determine whether there is a relationship between climate data and delta-7-stigmastenol values. According to this result, it has been determined that the delta-7-stigmastenol value is high when the annual average relative humidity is low and the annual average temperature is high. There is an urgent need to make forward-looking plans due to climate change.Conference Object Citation - WoS: 1Immunomodulatory Mechanisms of Astragalus Saponins(Wiley, 2021) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, DuyguArticle Citation - WoS: 5Citation - Scopus: 4Comparative Proteomic Analysis of Leishmania Parasites Isolated From Visceral and Cutaneous Leishmaniasis Patients(Cambridge University Press, 2021) Dinç, Melike; Yalçın, Talat; Çavuş, İbrahim; Özbilgin, AhmetLeishmaniasis is an infectious disease in which different clinical manifestations are classified into three main forms as visceral, cutaneous, and mucocutaneous. These disease forms are associated with parasite species of protozoan genus, Leishmania. For instance, Leishmania infantum and Leishmania tropica are typically linked with visceral (VL) and cutaneous (CL) leishmaniasis respectively, however these two species can also cause other form to a lesser extent. What is more alarming is this characteristic, which threatens classic diagnoses and therapies, is started to be acquired by other species. To address this issue, gel-based and gel-free proteomic analyses were carried out on the species, Leishmania infantum to determine the proteins differentiating between the parasites caused visceral and cutaneous leishmaniasis. In addition, Leishmania tropica parasites representing the typical cases for cutaneous leishmaniasis were included. Electrophoresis gels of parasites caused to visceral leishmaniasis were distinguishable from the others in terms of repetitive down-regulation on some specific locations. In addition, a distinct spot of an antioxidant enzyme, superoxide dismutase was shown up only on the gels of cutaneous leishmaniasis samples regardless of the species. In the gel-free approach, 37 proteins which were verified with a second database search using a different search engine, were distinguished from the comparison between VL and CL samples. Among them, 31 proteins for the CL group and 6 proteins for the VL group were determined differentially abundant. Two proteins from the gel-based analysis namely pyruvate kinase and succinly-coA:3-ketoacid-coenzyme A transferase analysis were encountered in the protein list of the CL group.Article Citation - WoS: 15Citation - Scopus: 14Electroactive Nanogel Formation by Reactive Layer-By Assembly of Polyester and Branched Polyethylenimine Via Aza-Michael Addition(American Chemical Society, 2021) Yıldırımkaraman, Öykü; Özenler, Sezer; Günay, Ufuk Saim; Durmaz, Hakan; Yıldız, Ümit HakanWe here demonstrate the utilization of reactive layer-by-layer (rLBL) assembly to form a nanogel coating made of branched polyethylenimine (BPEI) and alkyne containing polyester (PE) on a gold surface. The rLBL is generated by the rapid aza-Michael addition reaction of the alkyne group of PE and the -NH2 groups of BPEI by yielding a homogeneous gel coating on the gold substrate. The thickness profile of the nanogel revealed that a 400 nm thick coating is formed by six multilayers of rLBL, and it exhibits 50 nm roughness over 8 mu m distance. The LBL characteristics were determined via depth profiling analysis by X-ray photoelectron spectroscopy, and it has been shown that a 70-100 nm periodic increase in gel thickness is a consequence of consecutive cycles of rLBL. A detailed XPS analysis was performed to determine the yield of the rLBL reaction: the average yield was deduced as 86.4% by the ratio of the binding energies at 286.26 eV, (C CN-C bond) and 283.33 eV, (C C triple bond). The electrochemical characterization of the nanogels ascertains that up to the six-multilayered rLBL of BPEI-PE is electroactive, and the nanogel permeability had led to drive mass and charge transfer effectively. These results promise that nanogel formation by rLBL films may be a straightforward modification of electrodes approach, and it exhibits potential for the application of soft biointerfaces.