PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 2Citation - Scopus: 2Gas Phase Fragmentation Behavior of Proline in Macrocyclic B7 Ions(American Chemical Society, 2023) Taşoğlu, Çağdaş; Arslanoğlu, Alper; Yalçın, TalatThefragmentation characteristics of b (7) ionsproduced from proline-containing heptapeptides have been studiedin detail. The study has utilized the following C-terminally amidatedmodel peptides: PA(6), APA(5), A(2)PA(4), A(3)PA(3), A(4)PA(2), A(5)PA, A(6)P, PYAGFLV, PAGFLVY, PGFLVYA, PFLVYAG,PLVYAGF, PVYAGFL, YPAGFLV, YAPGFLV, YAGPFLV, YAGFPLV, YAGFLPV, YAGFLVP,PYAFLVG, PVLFYAG, A(2)PXA(3), and A(2)XPA(3) (where X = C, D, F, G, L, V, and Y, respectively). The resultshave shown that b (7) ions undergo head-to-tailcyclization and form a macrocyclic structure. Under the collision-induceddissociation (CID) condition, it generates nondirect sequence ionsregardless of the position of the proline and the neighboring aminoacid residues. This study highlights the unusual and unique fragmentationbehavior of proline-containing heptapeptides. Following the head-to-tailcyclization, the ring opens up and places the proline residue in theN-terminal position while forming a regular oxazolone form of b (2) ions for all peptide series. Then, the fragmentationreaction pathway is followed by the elimination of proline with itsC-terminal neighbor residue as an oxazolone (e.g., PXoxa) for all proline-containing peptide series.Editorial Citation - WoS: 1Citation - Scopus: 1Editorial: Biomaterial Applications in Soft Tissue Engineering and Replacement(Frontiers Media S.A., 2023) Hornyak, Istvan; Jedlovszky-Hajdu, Angela; Kehr, SedaThe research related to the application of biomaterials encompasses a large area within the field of tissue engineering and regenerative medicine (TERM), and this Research Topic was dedicated to the versatile possibilities in the use of biomaterials. The sum of 10 manuscripts were submitted to this Research Topic and six were selected for this Research Topic with the contribution of 35 authors, Four of the accepted manuscripts were original research articles and two were review articlesReview 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 Molecular Dynamics Simulation of Ssdna and Cationic Polythiophene(Elsevier, 2023) Nalıncı Bardak, Nehir; Kıbrıs, Erman; Demirci, Fethi Can; Elmacı Irmak, NuranIn this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak pi -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.Article Citation - WoS: 17Citation - Scopus: 19Strong Coupling of Carbon Quantum Dots in Liquid Crystals(American Chemical Society, 2022) Sarısözen, Sema; Polat, Nahit; Mert Balcı, Fadime; Güvenç, Çetin Meriç; Kocabaş, Çoşkun; Yağlıoğlu, Halime Gül; Balcı, SinanCarbon quantum dots (CDs) have recently received a tremendous amount of interest owing to their attractive optical properties. However, CDs have broad absorption and emission spectra limiting their application ranges. We herein, for the first time, show synthesis of water-soluble red emissive CDs with a very narrow line width (∼75 meV) spectral absorbance and hence demonstrate strong coupling of CDs and plasmon polaritons in liquid crystalline mesophases. The excited state dynamics of CDs has been studied by ultrafast transient absorption spectroscopy, and CDs display very stable and strong photoluminescence emission with a quantum yield of 35.4% and a lifetime of ∼2 ns. More importantly, we compare J-aggregate dyes with CDs in terms of their absorption line width, photostability, and ability to do strong coupling, and we conclude that highly fluorescent CDs have a bright future in the mixed light-matter states for emerging applications in future quantum technologies.Article Citation - WoS: 11Citation - Scopus: 12Colorimetric and Fluorometric Profiling of Advanced Glycation End Products(American Chemical Society, 2022) Ammanath, Gopal; Delachi, Carla Giorgia; Karabacak, Soner; Ali, Yusuf; Boehm, Bernhard O.; Yıldız, Ümit Hakan; Alagappan, Palaniappan; Liedberg, BoProfiling of advanced glycation end products (AGEs) is an emerging area of clinical significance for disease diagnosis and prognosis. Typically, concentrations of AGEs are estimated in laboratories by trained personnel using sophisticated equipment. Herein, a facile approach for colorimetric and fluorometric profiling of AGEs is reported for rapid and on-site analysis. The concentrations of AGE levels in plasma are estimated via changes in optical properties of polythiophenes (PTs) upon interaction with aptamers (Apts) in the presence and in the absence of AGEs. To validate the proposed approach, glyceraldehyde-derived AGEs (AGE class 1 [AGE1]), the biomarker associated with cardiovascular diseases and diabetes, are used as a model system. Colorimetric analysis yielded linear responses for AGE1 for clinically relevant concentration ranges between 1.5 and 300 μg/mL with a limit of detection (LOD) of ∼1.3 μg/mL. Subsequently, an approach utilizing PTs with four different pendant groups in conjunction with four different Apts is demonstrated for qualitative colorimetric profiling and for quantitative fluorometric profiling of up to four AGEs in clinical matrices. Principal component analysis (PCA) of fluorometric responses of AGE-spiked samples yielded distinct responses for the different AGEs tested. Thus, the proposed approach ascertains rapid profiling of spiked AGEs in plasma samples without the requirement of preanalytical processing and advanced instrumentation, thereby facilitating on-site diagnosis.Article Citation - WoS: 4Citation - Scopus: 4Recombinant Activated Protein C (rhapc) Affects Lipopolysaccharide-Induced Mechanical Compliance Changes and Beat Frequency of Mesc-Derived Cardiomyocyte Monolayers(Lippincott Williams and Wilkins Ltd., 2022) Temiz Artmann, Aysegül; Kurulgan Demirci, Eylem; Fırat, İpek Seda; Oflaz, Hakan; Artmann, Gerhard M.Background:Septic cardiomyopathy increases mortality by 70% to 90% and results in mechanical dysfunction of cells.Methods:Here, we created a LPS-induced in-vitro sepsis model with mouse embryonic stem cell-derived cardiomyocytes (mESC-CM) using the CellDrum technology which simultaneously measures mechanical compliance and beat frequency of mESCs. Visualization of reactive oxygen species (ROS), actin stress fibers, and mRNA quantification of endothelial protein C receptor (EPCR) and protease-activated receptor 1 (PAR1) before/after LPS incubation were used for method validation. Since activated protein C (APC) has cardioprotective effects, samples were treated with human recombinant APC (rhAPC) with/-out LPS predamage to demonstrate the application in therapeutic studies.Results:Twelve hours LPS treatment (5 μg/mL) increased ROS and decreased actin stress fiber density and significantly downregulated EPCR and PAR1 compared to control samples (0.26, 0.39-fold respectively). rhAPC application (5 μg/mL, 12 h) decreased ROS and recovered actin density, EPCR, and PAR1 levels were significantly upregulated compared to LPS predamaged samples (4.79, 3.49-fold respectively). The beat frequencies were significantly decreased after 6- (86%) and 12 h (73%) of LPS application. Mechanical compliance of monolayers significantly increased in a time-dependent manner, up to eight times upon 12-h LPS incubation compared to controls. rhAPC incubation increased the beat frequency by 127% (6h-LPS) and 123% (12h-LPS) and decreased mechanical compliance by 68% (12h-LPS) compared to LPS predamaged samples.Conclusion:LPS-induced contraction dysfunction and the reversal effects of rhAPC were successfully assessed by the mechanical properties of mESC-CMs. The CellDrum technology proved a decent tool to simulate sepsis in-vitro.Article Citation - WoS: 111Citation - Scopus: 97A General Approach To Composites Containing Nonmetallic Fillers and Liquid Gallium(American Association for the Advancement of Science, 2021) Wang, Chunhui; Gong, Yan; Cunning, Benjamin, V; Lee, Seunghwan; Le, Quan; Joshi, Shalik R.; Büyükçakır, OnurWe report a versatile method to make liquid metal composites by vigorously mixing gallium (Ga) with non-metallic particles of graphene oxide (G-O), graphite, diamond, and silicon carbide that display either paste or putty-like behavior depending on the volume fraction. Unlike Ga, the putty-like mixtures can be kneaded and rolled on any surface without leaving residue. By changing temperature, these materials can be stiffened, softened, and, for the G-O-containing composite, even made porous. The gallium putty (GalP) containing reduced G-O (rG-O) has excellent electromagnetic interference shielding effectiveness. GalP with diamond filler has excellent thermal conductivity and heat transfer superior to a commercial liquid metal-based thermal paste. Composites can also be formed from eutectic alloys of Ga including Ga-In (EGaIn), Ga-Sn (EGaSn), and Ga-In-Sn (EGaInSn or Galinstan). The versatility of our approach allows a variety of fillers to be incorporated in liquid metals, potentially allowing filler-specific fit for purpose materials.Article Citation - WoS: 9Citation - Scopus: 11Pcr-Free Methodology for Detection of Single-Nucleotide Polymorphism With a Cationic Polythiophene Reporter(American Chemical Society, 2021) Yücel, Müge; Koç, Altuğ; UÜgenalp, Ayfer; Akkoç, Gün Deniz; Ceyhan, Metin; Yıldız, Ümit HakanThis study presents a nonamplification-based nucleic acid assay for the detection of single-nucleotide polymorphism (SNP) associated with familial Mediterranean fever (FMF) besides polymerase chain reaction (PCR)-based methodologies. The major objective is to show the potential of the proposed assay for rapid screening of FMF in a Mediterranean region of 400 million population. The assay relies on binding difference of specially designed wild and mutant primers to the target genomic DNA, followed by determination of unbound primers by quick titration of a cationic polythiophene reporter. The fluorescent reporter exhibits signal transition from 525 to 580 nm in the presence of unbound primers, and it correlates the binding affinity of label-free primers to the homozygous wild and mutant genomes. As a proof of concept, 26 real samples are studied relying on the ON and OFF fluorescence signals of the cationic polythiophene reporter. The results are analyzed by principal component analysis (PCA), which provides clear separation of healthy and patient individuals. The further analysis by support vector machine (SVM) classification has revealed that our assay converges to 96% overall accuracy. These results support that the PCR-free nucleic acid assay has a significant potential for rapid and cost-effective screening of familial Mediterranean fever.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.