Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 4Citation - Scopus: 5Recent Progress in Wearable Extractive Sampling Technology(Elsevier, 2022) Kahremanoğlu, Kübra; Tosun Kurtalan, Hazal; Eroğlu, Ahmet Emin; Boyacı, EzelThe inevitable incline in the daily exposure to various chemicals has raised a necessity to monitor the body's exposure and biological responses to these stimuli more comprehensively and easily; conceivably, integrating novel designs, extractive phases, and state-of-the-art instrumentation with the primary aim of taking the chemical snapshot of the system. Wearable extractive devices are promising tools that are present in the analytical toolbox and address the abovementioned needs. These devices consist of a particular class of samplers that an individual can wear without limiting her/his daily life activities. In addition to being wearable, these devices show the ability to preconcentrate the analytes in an extractive phase while integrating the sampling and sample preparation. In addition to being imperative for personal exposure investigations, applications in diagnostic and prognostic health monitoring are among their emerging applications. Besides, in vivo soft samplers based on microextraction techniques provide non-invasive to low invasive approaches for non-lethal monitoring of various biosystems. Although in these applications they are not used in an ‘obvious way’ as wearable devices as they are not placed directly on the subject's skin and are instead immersed under the skin, in the scope of this review they will still be considered to provide a picture for future directions of extractive wearable devices. This review aims to cover the wearable extractive devices used in exposure studies (with a special focus on the last two years), in vivo, and in situ applications (with a focus on the last five years) where reliable information about the system is under interest.Article Citation - WoS: 43Citation - Scopus: 46Glucuronoxylan-Based Quince Seed Hydrogel: a Promising Scaffold for Tissue Engineering Applications(Elsevier, 2021) Güzelgülgen, Meltem; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, AhuNatural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuron-oxylanbased quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH and crosslinker glutaraldehyde (GTA) concentrations. Structural characterization of QSH was done by Fourier Transform Infrared Spectroscopy (MR). Furthermore, morphological and mechanical investigation of QSH was performed by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The protein adsorption test revealed the suitability of QSH for cell attachment. Biocompatibility of QSH was confirmed by culturing NIH-3T3 mouse fibroblast cells on it. Cell viability and proliferation results revealed that optimum parameters for cell viability were 2 mg mi(-1)of QSH and 0.03 M GTA. SEM and DAPI staining results indicated the formation of spheroids with a diameter of approximately 300 pm. Furthermore, formation of extracellular matrix (ECM) microenvironment was confirmed with the Collagen Type-I staining. Here, it was demonstrated that the fabricated QSH is a promising scaffold for 3D cell culture and tissue engineering applications provided by its highly porous structure, remarkable swelling capacity and high biocompatibility. (C) 2021 Published by Elsevier B.V.Article Citation - WoS: 14Citation - Scopus: 16Bodipy-Based Organic Color Conversion Layers for Wleds(Elsevier, 2020) Yüce, Hürriyet; Güner, Tuğrul; Dartar, Suay; Kaya, Beraat Umur; Emrullahoğlu, Mustafa; Demir, Mustafa MuammerThe usage of organic dyes in phosphor conversion layer of WLED is an attractive approach since they have high molar extinction coefficient and photostability. Various types of organic pigments have been employed for this purpose such as BODIPY, perylene diimide, Rhodamine B, pyrene, Nile red, etc. Among those, BODIPY-based organic dyes appear to be promising candidate for white light generation. In this work, for the first time, red and green emitting BODIPY-based organic molecules have been used as colour conversion layer. These molecules were associated with PMMA in DMF solution and the resulting solution was subjected to electrospinning. Colorful electrospun mats were embedded into PDMS matrix and their free-standing PDMS composite films were used as color conversion layers over blue LED to produce white light such that CRI of 95 and CCT of 4200 K was achieved. These values show that BODIPY-based organic molecules containing fiber composites are promising candidates to be used as color conversion layers for white light applications.Article Citation - WoS: 10Citation - Scopus: 11A New Drug Testing Platform Based on 3d Tri-Culture in Lab-On Devices(Elsevier, 2020) Gökçe, Begüm; Akçok, İsmail; Çağır, Ali; Pesen Okvur, DevrimDrug discovery has a 90% rate of failure because preclinical platforms for drug testing do not mimic the in vivo conditions. Doxorubicin (DOX) is a commonly used drug to treat breast cancer patients even though it has side effects. Lab-on-a-chip (LOC) devices provide spatial control at the micrometer scale and can thus emulate the cancer microenvironment. Here, using a multidisciplinary approach, a new drug testing platform based on 3D tri-culture in LOC devices was developed. Breast cancer cells alone or with normal mammary epithelial cells and macrophages were cultured in matrigel in LOC devices. The platform was used to test DOX and (R)-4'-methylklavuzon (KLA), which is a new anti-cancer drug candidate. Results showed that DOX and KLA were equally effective on breast cancer cells in 3D monoculture. KLA produced 26% less death for breast cancer cells than DOX in 3D tri-culture. More importantly, DOX was not selective between breast cancer cells and normal mammary epithelial cells in 3D tri- culture whereas KLA caused 56% less cell death than DOX for normal mammary epithelial cells. Results strongly recommend that 3D tri-culture in LOC devices be used for assessment of drug toxicity at the preclinical stage.Article Citation - WoS: 39Citation - Scopus: 44Identification and Characterization of Novel Thermostable Alpha-Amylase From Geobacillus Sp. Gs33(Elsevier, 2020) Burhanoğlu, Tülin; Sürmeli, Yusuf; Şanlı Mohamed, GülşahIn this study, the heterologous expression and biochemical characterization of a thermostable alpha-amylase from Geobacillus sp. GS33 was investigated. The recombinant alpha-amylase was overexpressed in Escherichia coli BL21 (lambda DE) and purified via anion exchange and size-exclusion chromatography. The purified alpha-amylase had a molecular weight of about 60 kDa, and was active in a broad range of pH 3-10 and temperature (40-90 degrees C) withmaximumactivity at pH 7-8 and 60 degrees C. The enzyme retained 50% residual activity at 65 degrees C, but only 20% at 85 degrees C after 16 h. At pH 9 and pH 7, the residual activity at 65 degrees C was 50% and 30%, respectively. The enzymewas remarkably activated by Co2+, Ca2+, Mg2+, PMSF, DTT, and Triton X-100, but partially inhibited by Cu2+, methanol, hexane, ethanol, acetone, SDS, and Tween 20. A molecular phylogeny analysis showed that the enzyme's amino acid sequence had the closest connection with an alpha-amylase from Geobacillus thermoleovorans subsp. stromboliensis nov. 3D-structure-based amino acid sequence alignments revealed that the three catalytic residues (D217, E246, D314) and the four Ca2+ ion coordination residues (N143, E177, D186, H221) were conserved in alpha-amylase from Geobacillus sp. GS33. The temperature stability and neutral pH optimum suggest that the enzyme may be useful for industrial applications. (C) 2020 Elsevier B.V. All rights reserved.Article 2’-Methylklavuzon Causes Lipid-Lowering Effects on A549 Non-Small Cell Lung Cancer Cells and Significant Changes on Dna Structure Evidenced by Fourier Transform Infrared Spectroscopy(Elsevier, 2020) Ceylan, Çağatay; Aksoy, Hatice Nurdan; Çağır, Ali; Çetinkaya, HakkıVarious chemical agents are used in the treatment of Non-Small Cell Lung Cancer (NSCLC). 2?-methylklavuzon was proposed as a potential chemotherapeutic agent in cancer treatment based on its topoisomerase inhibition activity. In this study the cellular effects of 2?-methylklavuzon was evaluated on A549 cancer cells using FTIR spectroscopy. 2?-methylklavuzon induced significant changes on both the whole cell lyophilizates and the lipid extracts of the A549 lung cancer cells. 2?-methylklavuzon caused significant structural changes in A549 cell DNA structure: T, A and G DNA breathing modes are lost after the drug application indicating the loss of topoisomerase activity. The level of transcription and RNA synthesis was enhanced. 2?-methylklavuzon induced single stranded DNA formation evidenced by the increase in the ratio of asymmetric/symmetric phosphate stretching modes. 2?-methylklavuzon induced band shifts only in the asymmetric mode of phosphate bonds not in the symmetrical phosphate bond stretching. 2?-methylklavuzon induced A form of DNA topography. In addition to the changes in the DNA structure and transcription 2?-methylklavuzon also caused lipid-lowering effect in A549 cancer cells. 2?-methylklavuzon suppressed lipid unsaturation, however, it induced formation of lipids with ring structures. 2?-methylklavuzon suppressed phosphate-containing lipids significantly and decreased carbonyl containing lipids and cholesterol slightly. 2?-methylklavuzon caused increases in the hydrocarbon chain length. Overall, 2?-methylklavuzon can be used as a lipid-lowering compound in the treatment of NSCLC and other cancer therapies. © 2020 Elsevier B.V.Article Citation - WoS: 39Citation - Scopus: 37Flow-Through Colorimetric Assay for Detection of Nucleic Acids in Plasma(Elsevier, 2019) Ammanath, Gopal; Yeasmi, Sanjida; Srinivasulu, Yuvasri; Vats, Mukti; Cheema, Jamal Ahmed; Nabilah, Fairuz; Liedberg, Bo; Yıldız, Ümit HakanA flow-through colorimetric assay for detection of nucleic acids in plasma is reported. The proposed assay features an array of four polyvinylidene fluoride (PVDF) membranes impregnated with cationic poly (3-alkoxy-4-methylthiophene) (PT) as an optical reporter. The sensing strategy is based on monitoring the changes in optical properties of PT, upon complexation with target nucleic acids in the presence and in the absence of their corresponding complementary peptide nucleic acids (PNAs). As a proof of concept, the proposed methodology is validated using two biomarkers; lung cancer associated microRNA (mir21) and hepatitis B virus DNA (HBV-DNA). The flow-through colorimetric assay enabled detection of mir21 and HBV-DNA in plasma without requiring tedious sample pre-treatment and clean up protocols. Colorimetric responses for mir21 and HBV-DNA were obtained at nanomolar concentrations over five orders of magnitudes (from 1 nM to 10 mu M), with a limit of detection of -0.6 nM and -2 nM in DI water and plasma, respectively. A logic gate system was developed to utilize the colorimetric assay responses as inputs for discrimination of mir21 and HBV-DNA and subsequently to obtain a profile of nucleic acids in samples that exceed respective clinical threshold limits, thereby enabling rapid and point of care (POC) disease diagnosis. Furthermore, the proposed methodology can be utilized for detection of a large number of nucleic acids in plasma by extending the array of PT impregnated membranes incorporated with their corresponding complementary PNAs. (C) 2019 Elsevier B.V. All rights reserved.Article Citation - WoS: 5Citation - Scopus: 5Synthesis and Structures of 1,3,2,4,5-Diazatriborolidines(Elsevier, 2019) Fırıncı, Erkan; Sevinçek, Resul; Bursalı, Banu; Özgener, Hüseyin; Burgaz, Osman; Şen, Ceren; Şahin, YükselThe derivatives of diazatriborolidine are a class of 5-membered heterocyclic compounds containing a ring with two nitrogen atoms and three boron atoms. The 1,3,2,4,5-diazatriborolidine derivatives were synthesized from 1,2-bis(N-lithium-arylamino) diborane(4) and dichloro-dimethylaminoborane with high yield. The structures of these new derivatives were determined using nuclear magnetic resonance (NMR) spectroscopy. The molecular structures of 3a, 3b, 3d, 4b and 4c were determined using single-crystal X-ray diffraction. Their structural features were discussed and compared with similar diazatriborolidines. In addition, the enthalpy of formation of B and N atoms containing five membered heterocycles were calculated theoretically for the first time. Also, an easy and efficient synthesis route has been reported for preparation of 1,3,2,4,5-diazatriborolidine derivatives.Article Citation - WoS: 90Citation - Scopus: 101A Rapid Atr-Ftir Spectroscopic Method for Classification of Gelatin Gummy Candies in Relation To the Gelatin Source(Elsevier, 2019) Çebi, Nur; Doğan, Canan Ekinci; Ekin Meşe, Ayten; Özdemir, Durmuş; Arıcı, Muhammet; Sağdıç, OsmanGelatin is widely used in gummy candies because of its unique functional properties. Generally, porcine and bovine gelatins are used in the food industry. FTIR-ATR combined with chemometrics analysis such as hierarchical cluster analysis (HCA) (OPUS Version 7.2 software), principal component analysis (PCA) (OPUS Version 7.2 software) and partial least squares-discriminant analysis (PLS-DA) (Matlab R2017b) were used for classification and discrimination of gelatin gummy candies related to their gelatin source. The spectral region between 1734 and 1528 cm(-1) was selected for chemometric analysis. The potential of FTIR spectroscopy for determination of bovine and porcine source in gummy candies was examined and validated by a real-time polymerase chain reaction (PCR) method. Twenty commercial samples were tested by developed ATR-FTIR methodology and RT-PCR technique, mutually confirming and supporting results were obtained. Gummy candies were classified and discriminated in relation to the bovine or porcine source of gelatin with 100% success without any sample preparation using FTIR-ATR technique.Article Citation - WoS: 17Citation - Scopus: 19Pixelated Colorimetric Nucleic Acid Assay(Elsevier, 2020) Aydın, Hakan Berk; Cheema, Jamal Ahmed; Arnmanath, Gopal; Toklucu, Cihan; Yücel, Müge; Özenler, Sezer; Yıldız, Ümit HakanConjugated polyelectrolytes (CPEs) have been widely used as reporters in colorimetric assays targeting nucleic acids. CPEs provide naked eye detection possibility by their superior optical properties however, as concentration of target analytes decrease, trace amounts of nucleic acid typically yield colorimetric responses that are not readily perceivable by naked eye. Herein, we report a pixelated analysis approach for correlating colorimetric responses of CPE with nucleic acid concentrations down to 1 nM, in plasma samples, utilizing a smart phone with an algorithm that can perform analytical testing and data processing. The detection strategy employed relies on conformational transitions between single stranded nucleic acid-cationic CPE duplexes and double stranded nucleic acid-CPE triplexes that yield distinct colorimetric responses for enabling naked eye detection of nucleic acids. Cationic poly[N,N,N-triethyl-3-((4-methylthiophen-3-yl)oxy)propan-1-aminium bromide] is utilized as the CPE reporter deposited on a polyvinylidene fluoride (PVDF) membrane for nucleic acid assay. A smart phone application is developed to capture and digitize the colorimetric response of the individual pixels of the digital images of CPE on the PVDF membrane, followed by an analysis using the algorithm. The proposed pixelated approach enables precise quantification of nucleic acid assay concentrations, thereby eliminating the margin of error involved in conventional methodologies adopted for interpretation of colorimetric responses, for instance, RGB analysis. The obtained results illustrate that a ubiquitous smart phone could be utilized for point of care colorimetric nucleic acids assays in complex matrices without requiring sophisticated software or instrumentation.