Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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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 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: 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: 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: 35Citation - Scopus: 36Understanding Radiative Transitions and Relaxation Pathways in Plexcitons(Cell Press, 2021) Finkelstein-Shapiro, Daniel; Mante, Pierre-Adrien; Sarısözen, Sema; Wittenbecher, Lukas; Minda, Iulia; Balcı, Sinan; Pullerits, TonuMolecular aggregates on plasmonic nanoparticles have emerged as attractive systems for the studies of polaritonic light-matter states, called plexcitons. Such systems are tunable, scalable, easy to synthesize, and offer sub-wavelength confinement, all while giving access to the ultrastrong light-matter coupling regime, promising a plethora of applications. However, the complexity of these materials prevented the understanding of their excitation and relaxation phenomena. Here, we follow the relaxation pathways in plexcitons and conclude that while the metal destroys the optical coherence, the molecular aggregate coupled to surface processes significantly contributes to the energy dissipation. We use two-dimensional electronic spectroscopy with theoretical modeling to assign the different relaxation processes to either molecules or metal nanoparticle. We show that the dynamics beyond a few femtoseconds has to be considered in the language of hot electron distributions instead of the accepted lower and upper polariton branches and establish the framework for further understanding.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.