Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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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: 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: 2Tuning the Solid Phase Fluorescence Emission From Long Wavelength Visible To Near-Infrared in Oxazol-5 Derivatives: Structure–property Relationship, Theoretical and Experimental Studies(Springer, 2023) Nazlı, İbrahim Hanif; Yakalı, Gül; Topkaya, Derya; İzmirli, Merve; Uzun, Sema Demirci; Alp, SerapMost of the fluorescent molecules among organic π-conjugated materials show blue or green emission in the solid phase but few of them emit red-shifted visible and near-infrared light in the material science. To create molecules emitting for this feature, two π-conjugated oxazol-5-one derivatives containing donor (OCH3) and acceptor groups (NO2) were synthesized. Their optical and charge-transport properties were investigated through experimental and theoretical methods including the single crystal X-ray crystallography, Hirshfeld Surface Analysis, photophysical studies and Density Functional Theory (DFT), respectively. In addition, FT-IR, 1H-NMR, 13C-NMR spectroscopy, cyclic voltammetry (CV) measurements were performed. According to our results, both molecules may provide the significant pathway of development of long wavelength visible and red emissive features in solid phase with the aggregation induced enhanced emission (AIEE) properties particularly in the fields of OLEDs, optical communication, defence and bioimaging.Article Citation - WoS: 49Citation - Scopus: 54Highly Porous Poly(o-Phenylenediamine) Loaded Magnetic Carboxymethyl Cellulose Hybrid Beads for Removal of Two Model Textile Dyes(Springer, 2022) Arıca, Tuğçe Aybüke; Balcı, Fadime Mert; Balcı, Sinan; Arıca, Mehmet YakupEnsuring the removal of complex dyes from wastewater is a topic of great interest as it is vital for the environment. The present study reports a facile preparation method for poly(o-phenylenediamine) [p(o-PDA)] micro-particles loaded to magnetic carboxymethyl cellulose (CMC) hydrogel beads as adsorbents. The prepared products were characterized by FTIR, TGA, VSM, SEM, BET, and zeta sizer. The Fe3O4@p(o-PDA)@CMC beads were used for the removal of Reactive Blue 4 (RB-4) and Congo Red (CR) textile dyes from an aqueous medium. Different factors, such as adsorbent dose, initial pH, ionic strength, contact time, temperatures, and initial RB-4 and CR concentrations were examined. The maximum adsorption capacities of the RB-4 dye and CR at optimum pH 5 reached 398.7 and 524.6 mg/g in 120 min, respectively. The adsorption of RB-4 and CR on the hybrid magnetic beads can be due to the electrostatic, hydrogen bonding, and π-π interactions. Moreover, the magnetic hybrid beads showed easy regeneration ability and good reusability. The adsorbent can be a very good candidate for the efficient removal of micro-pollutant from wastewater.Article Citation - WoS: 14Citation - Scopus: 19Influence of Carbon Nanotube Inclusions To Electrical, Thermal, Physical and Mechanical Behaviors of Carbon-Fiber Abs Composites(Springer, 2022) Akar, Alinda Öykü; Yıldız, Ümit Hakan; Tirkeş, Seha; Tayfun, Ümit; Hacıvelioğlu, FerdaAcrylonitrile–butadiene–styrene (ABS) terpolymer was compounded with short carbon fiber (CF) and carbon nanotube (CNT) using a micro-extruder followed by the injection molding process. Composite samples were fabricated with loading ratios of 20 wt.% CF and 0.1, 0.5 and 1.0 wt.% of CNT. Mechanical, electrical, thermo-mechanical, thermal, melt-flow, and structural investigations of ABS-based composites were conducted by performing tensile, impact, hardness, and wear tests, conductive atomic force microscopy (AFM), dynamic mechanical analysis (DMA), thermal gravimetric analysis (TGA), melt flow rate test (MFR), scanning electron microscopy (SEM) characterization techniques, respectively. According to mechanical test data of resultant composites including tensile and impact test findings, CNT additions led to the remarkable increase in tensile strength and impact resistance for CF reinforced ABS composites. The formation of synergy between CNT nanoparticles and CF was confirmed by electrical conduction results. The conductive path in ABS/CF composite system was achieved by the incorporation of CNT with different loading levels. SEM micrographs of composites proved that CNT nanoparticles exhibited homogeneous dispersion into ABS matrix for lower loadings. Graphical abstract: [Figure not available: see fulltext.].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.