Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
Browse
10 results
Search Results
Review Citation - WoS: 116Citation - Scopus: 125Salivary Biomarkers: Novel Noninvasive Tools To Diagnose Chronic Inflammation(Springer, 2023) Dongiovanni, Paola; Meroni, Marica; Casati, Sara; Goldoni, Riccardo; Thomaz, Douglas Vieira; Kehr, Nermin Seda; Galimberti, DanielaSeveral chronic disorders including type 2 diabetes (T2D), obesity, heart disease and cancer are preceded by a state of chronic low-grade inflammation. Biomarkers for the early assessment of chronic disorders encompass acute phase proteins (APP), cytokines and chemokines, pro-inflammatory enzymes, lipids and oxidative stress mediators. These substances enter saliva through the blood flow and, in some cases, there is a close relation between their salivary and serum concentration. Saliva can be easily collected and stored with non-invasive and cost-saving procedures, and it is emerging the concept to use it for the detection of inflammatory biomarkers. To this purpose, the present review aims to discuss the advantages and challenges of using standard and cutting-edge techniques to discover salivary biomarkers which may be used in diagnosis/therapy of several chronic diseases with inflammatory consequences with the pursuit to possibly replace conventional paths with detectable soluble mediators in saliva. Specifically, the review describes the procedures used for saliva collection, the standard approaches for the measurement of salivary biomarkers and the novel methodological strategies such as biosensors to improve the quality of care for chronically affected patients.Article Citation - WoS: 7Citation - Scopus: 10Enhanced Light–matter Interaction in a Hybrid Photonic–plasmonic Cavity(Springer, 2021) Gökbulut, Belkıs; İnanç, Arda; Topçu, Gökhan; Özçelik, Serdar; Demir, Mustafa Muammer; İnci, Mehmet NaciStrongly concentrated optical fields around a metal nanoparticle in the close vicinity of a dipole noticeably facilitate dramatic changes in the localized density of states due to hybrid photonic–plasmonic mode couplings as compared to that of the pure cavity mode fields. Significant variations of the field intensity in the presence of the metal nanoparticle elucidate enhanced light–matter interaction in a hybrid structure. The enhancement factor of the light–matter interaction is studied through the single-atom cooperativity parameter, which is directly proportional to the ratio of the fluorescence lifetimes of the off-resonant and on-resonant emission. A compact and cost-effective hybrid device, which includes a microfiber cavity, supporting whispering gallery modes, and a well-defined solid nanostructure, consisting of a gold nanoparticle core, overcoated by a silica shell, and decorated with CdS/CdSe quantum dots, is demonstrated to offer an outstanding potential for the enhancement of light–matter interaction. Surface plasmons of a gold nanoparticle, placed inside a hollow cylindrical nanostructure at the surface of a microfiber, are activated upon excitation of the dipoles of the quantum emitters, which are on-resonance with the whispering gallery mode. Time-resolved experiments demonstrate that the single-atom cooperativity parameter of the quantum dots is enhanced by a factor of about 4.8 in the presence of the gold nanoparticle being simultaneously in strong interaction with the cavity mode field and the metal nanoparticle’s surface plasmons.Correction Correction To: Enhanced Light–matter Interaction in a Hybrid Photonic–plasmonic Cavity(Springer, 2022) Gökbulut, Belkıs; İnanç, Arda; Topçu, Gökhan; Özçelik, Serdar; Demir, Mustafa Muammer; İnci, Mehmet NaciIn this article the statement in the Funding information section was incorrect. The correct Funding information is as follows. ‘Dr Belkıs Gökbulut acknowledges TUBITAK for the financial support provided under Contract Number 120F323’.Article Citation - WoS: 11Citation - Scopus: 16Purification and Biochemical Characterization of a Novel Thermostable Serine Protease From Geobacillus Sp. Gs53(Springer, 2021) Şanlı Mohamed, Gülşah; Güracar Baykara, Seden; Sürmeli, YusufProteases account for approximately 60% of the enzyme market in the world, and they are used in various industrial applications including the detergent industry. In this study, production and characterization of a novel serine protease of thermophilic Geobacillus sp. GS53 from Balcova geothermal region, Izmir, Turkey, were performed. The thermostable protease was purified through ammonium sulfate precipitation and anion-exchange chromatography. The results showed that the protease had 137.8 U mg(-1) of specific activity and optimally worked at 55 C-o and pH 8. It was also active in a broad pH (4-10) and temperature (25-75 degrees C) ranges. The protease was highly stable at 85 degrees C and demonstrated relative stability at pH 4, 7, and 10. Also, the enzyme had high stability against organic solvents and surfactants; enzyme relative activity did not decrease below 81% upon preincubation for 10 min. Ca2+, Cu2+, and Zn2+ ions slightly induced protease activity. The protease was highly specific to casein, skim milk, Hammerstein casein, and BSA substrates. These results revealed that the protease might have a potential effect in a variety of industrial fields, especially the detergent industry, because of its high thermostability and stability to surfactants.Article Citation - WoS: 6Citation - Scopus: 5Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk(Springer, 2021) Kıbrıs, Erman; Nalıncı Barbak, Nehir; Elmacı Irmak, NuranIn the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.Article Citation - WoS: 7Citation - Scopus: 8Investigation of Oxygen Evolution Reaction Performance of Silver Doped Ba0.5sr0.5co0.8fe0.2o3-Delta Perovskite Structure(Springer, 2020) Göl, Emre Yusuf; Aytekin, Ahmet; Özkahraman, Ecem Ezgi; Karabudak, EnginStudies on novel electrochemical catalyst synthesis for efficient oxygen evolution reaction (OER) attract the attention of researchers. In general, changing of synthesis method and the doping metal affect the electrochemical activities of BSCF. In this work, silver doped Ba0.5Sr0.5Co0.8Fe0.2O3-delta (BSCF-Ag) perovskite structure is shown to be a better electrocatalyst for oxygen evolution reaction (OER) due to its lower overpotential and extended durability. BSCF structure was synthesized by the EDTA-citric acid method. Appropriate amount of Ba(NO3)(2) and EDTA were dissolved 0.1 M NH4OH solution. Nitrate salts of other metals were dissolved in distilled water, then mixed with prepared Ba(NO3)(2) solution. The mixture was stirred at 70 degrees C until gelation occurred. The gelled samples obtained were baked in a drying oven at 250 degrees C for 24 h before being calcined at 1000 degrees C for 12 h. To achieve a current density of 10 mA cm(-2), BSCF-Ag has required an overpotential of 0.36 V, which is very low compared to BSCF. To determine the stability of BSCF-Ag, continuous chronopotentiometry tests were carried out for 5 h and at a constant current density of 10 mA cm(-2). BSCF-Ag was characterized by XRD, SEM, and XPS.Book Part Citation - Scopus: 6Recent Advances in Chitosan-Based Systems for Delivery of Anticancer Drugs(Springer, 2020) Polat, Mehmet; Polat, HürriyetProblems in transporting drug molecules to tumor sites in required dose or constitution lead to low efficacy and significant side effects. Shielding the drug molecules in micelles, liposomes, or nanoparticles is a major line of investigation to improve chemotherapeutic treatment. Though compatibility for proper envelopment of the drug and timely release at the tumor site are required of such a carrier, protecting its own physicochemical and morphological integrity during transport is another precondition. Because of its superior polymerization capability, biocompatibility, pH dependence, and charging characteristics, chitosan has been in the forefront of potential drug carriers. Numerous synthesis routes for chitosan-based nanocarriers have been suggested to the extent that a search of the literature published since 2000 with the keywords “novel + nano + chitosan” in the title results in 527 articles, indicating the bewildering quality and quantity of the new information. This review was carried out not only to peruse this large amount of work on chitosan-based anticancer drug delivery but also to extract manageable patterns from numerous synthesis routes. The main conclusion is that the synthesis methods suggested in literature can be combined into two main routes, and the degree of hydrophobicity of the drug determines which route should be followed. © Springer Nature Singapore Pte Ltd. 2019.Conference Object Citation - WoS: 2Citation - Scopus: 1Determination of Aluminum Oxide Thickness on the Annealed Surface of 8000 Series Aluminum Foil by Fourier Transform Infrared Spectroscopy(Springer, 2017) İnanç Uçar, Özlem; Ekin Meşe, Ayten; Birbaşar, Onur; Dündar, Murat; Özdemir, DurmuşAluminum foil produced with prescribed thermomechanical processing route develop oxide film. Alloy chemistry and annealing practices, particularly its duration and exposed temperature, determine the characteristics of the oxide film. The magnitude and characteristics of the oxide film may impair surface features leading to serious problems in some applications, such as coating, printing and in some severe cases failure in formability. Therefore, it is important for the rolling industry to be able to monitor the oxide formation on the foil products and quantify its thickness. Well known methods to measure an oxide thickness that is in the order of nanometer, require meticulous sample preparation techniques, long duration for measurements and sophisticated equipment. However, in this study, a simple and rapid grazing angle attenuated total reflectance infrared (GA-ATR-FTIR) spectroscopic method combined with chemometrics multivariate calibration has been developed for the oxide thickness determination which is validated with x-ray photoelectron spectroscopy (XPS). 3000 and 8000 series aluminum foil materials which were produced by twin roll casting technique were used in this study. Foil samples were annealed at various different temperatures and annealing times in a laboratory scale furnace. Immediately after collecting GA-ATR-FTIR spectra, the 3000 series alloy samples were sent to a laboratory where XPS reference oxide thickness measurements had been performed. Partial Least Squares (PLS) method was used to develop a multivariate calibration model based on FTIR spectra and XPS reference oxide thickness values in order to predict the aluminum oxide thickness. The correlation coefficient of XPS reference oxide thickness values versus grazing angle ATR-FTIR based PLS predicted values was found as 0.9903 the standard error of cross validation (SECV) was found to be 0.29 nm in range of 4.9–14.0 nm for Al2O3. In addition, the standard error of prediction (SEP) for the validation set was 0.24 nm with the model generated with three principal components (PCs). © The Minerals, Metals & Materials Society 2017.Article Citation - WoS: 18Citation - Scopus: 23A Thermophilic ?-L From Geobacillus Vulcani Gs90: Heterologous Expression, Biochemical Characterization, and Its Synergistic Action in Fruit Juice Enrichment(Springer, 2018) İlgü, Hüseyin; Sürmeli, Yusuf; Şanlı Mohamed, Gülşahα-l-Arabinofuranosidases with an orchestral action of xylanolytic enzymes degrades the xylan in plant cell wall. In this study, heterologous expression, biochemical characterization, and synergistic action of α-l-Arabinofuranosidase from previously identified.Geobacillus vulcani GS90 (GvAbf) was investigated. The recombinant α-l-Arabinofuranosidase was overexpressed in Escherichia coli BL21 (λDE) and purified via His-tag Ni-affinity and size-exclusion chromatography. Optimum activity of the purified α-l-Arabinofuranosidase was obtained at pH 5 and at 70 °C. The GvAbf was active in a broad pH and temperature ranges; pH 4–9 and 30–90 °C, respectively. In addition, it retained most of its activity after an hour incubation at 70 °C and remained relatively stable at pH 3–6. GvAbf was quite stable against various metal ions. The kinetic parameters of GvAbf was obtained as Vmax and Km; 200 U/mg and 0.2 mM with p-nitrophenyl-α-l-arabinofuranoside and 526 U/mg and 0.1 mM with sugar beet arabinan, respectively. The synergistic action of GvAbf was studied with commercially available xylanase on juice enrichment of apples, grapes, oranges, and peaches. The best juice enrichment in terms of clarity, reducing sugar content, and yield, was achieved with GvAbf and xylanase together compared to treatment with xylanase and GvAbf alone in all fruits. The treatment with GvAbf and xylanase together lead to an increased juice yield by 26.56% (apple), 30.88% (grape), 40.00% (orange) and 32.20% (peach) as well as having a significant effect on juice clarity by an increase of % transmittance 47.26, 25.98, 41.77, and 44.97, respectively. The highest reducing sugar level of fruit juices also obtained with GvAbf and xylanase together compared to treatment with xylanase and GvAbf alone in all types of fruits. GvAbf and xylanase together as simultaneous synergistic manner may have an exciting potential for application in fruit juice processing.Article Citation - WoS: 9Citation - Scopus: 9Tuning Photoinduced Intramolecular Electron Transfer by Electron Accepting and Donating Substituents in Oxazolones(Springer, 2013) Öztürk, Gülsiye; Karabıyık, Hasan; Aygün, Muhittin; Alp, Serap; Özçelik, SerdarThe solvatochromic and spectral properties of oxazolone derivatives in various solvents were reported. Fluorescence spectra clearly showed positive and negative solvatochromism depending on substituents. The solvatochromic plots and quantum chemical computations at DFT-B3LYP/6-31+G(d,p) level were used to assess dipole moment changes between the ground and the first excited singlet-states. The electron accepting nitro substituent at the para-position increased the π-electron mobility, however, the 3,5-dinitro substituent decreased the π-electron mobility as a result of inverse accumulation of the electronic density as compared with that of its ground state. Experimental and computational studies proved that the photoinduced intramo- lecular electron transfer (PIET) is responsible for the observed solvatochromic effects. We demonstrate that PIET can be finely tailored by the position of the electron accepting and donating substituents in the phenyl ring of the oxazolone de- rivatives.We propose that the photoactive CPO derivatives are new molecular class of conjugated push-pull structures using azlactone moiety as the π-conjugated linker and may find applications in photovoltaic cells and light emitting diodes.