Scopus İndeksli Yayınlar Koleksiyonu

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  • Article
    Development of Resistant Starch Type-5 and Its Utilization in Cookie-Preparation
    (North University Center Baia Mare, 2025-11-30) Oskaybas-Emlek, Betul; Ozbey, Ayse; Kahraman, Kevser
    The objective of this study was the production of resistant starch type-5 (RS-5), its characterization, and utilization in cookie making. In first part of the study, the effects of starch-fatty acid complex formation (RS-5) between tapioca starch and lauric acid on the structure, digestibility, thermal and morphological properties of tapioca starch were investigated. X-ray diffraction revealed that the RS-5 had a V-type crystalline pattern. FT-IR analysis showed that a distinctive peak at 2846 cm-1 was only observed in RS-5. The resistant starch (RS) content of native starch increased from 22.76% to 28.02% with RS-5 formation. In the second part of the study, the RS-5 was added as a replacement for wheat flour with 10%, 20%, and 30% compared to control sample made with 100% wheat flour in cookie-making. The effects of RS-5 replacement of cookie samples on some physicochemical, estimated glycemic index (eGI) value, physical, and hardness properties were determined. Compared to control cookie, the cookie samples included RS-5 had lower hardness value, higher spread ratio. The eGI value of cookie samples was slightly decreased with the replacement with RS-5. The results demonstrated that the RS-5 has good potential for developing softer cookie with no adverse impact on eGI value.
  • Article
    Citation - WoS: 1
    Comprehensive Prediction of FBN1 Targeting Mirnas: A Systems Biology Approach for Marfan Syndrome
    (Galenos Publishing House, 2025-09-22) Orhan, M.E.; Demirci, Y.M.; Saçar Demirci, M.D.S.; Demirci, Muserref Duygu Sacar
    Objective: Marfan syndrome (MFS) is a genetic connective tissue disorder primarily caused by mutations in the FBN1 gene. Emerging evidence highlights the regulatory role of microRNAs (miRNAs) in modulating gene expression in MFS, but a systematic investigation into miRNAs targeting FBN1 is lacking. This study aimed to comprehensively identify miRNAs interacting with the FBN1 transcript to reveal potential molecular regulators and therapeutic targets. Methods: Human miRNA sequences were retrieved from miRBase (Release 22.1), and the canonical FBN1 transcript (RefSeq: NM_000138.5) was used for target prediction. Computational interaction analysis was conducted using the psRNATarget server with stringent parameters to detect potential miRNA binding sites. Expression profiles and disease associations of the top candidate miRNAs were further investigated through database integration and literature review. Results: Out of 2656 human mature miRNAs analyzed, 251 were predicted to bind FBN1, with the hsa-miR-181 family exhibiting the highest number of predicted interactions. Evidence from the literature highlighted dysregulation of hsa-miR-181 expression in MFS patients, suggesting a functional role in disease pathophysiology. Conclusion: This study identifies key members of the hsa-miR-181 family as post-transcriptional regulators of FBN1, offering new insights into miRNA-driven mechanisms in MFS. These findings support the potential of RNA-based diagnostics and therapeutic strategies targeting miRNA-FBN1 interactions. ©Copyright 2025 The Author.
  • Article
    Use of Confocal Microscopy to Monitor Structural Transformations in Nanopillars Based on DNA and CdSe/CdZnSe Quantum Dots
    (Springer, 2023-06-24) Motevich, I. G.; Erdem, T.; Akrema, A.; Maskevich, S. A.; Strekal, N. D.
    Chip system prototypes in the form of nanopillars were created from DNA complexes with CdSe/CdZnSe/ZnS quantum dots immobilized on a plasmonic gold fi lm by the use of vacuum deposition technology and inorganic synthesis. The design and presence of terminal DNA labeled with Cy3 cyanine dyes makes it possible to carry out the hybridization reaction of this terminal strand with complementary DNA and to control the process by variation of the giant Raman scattering (GRS) and the fluorescence signal. The effect of molecular recognition of complementary DNA is accompanied by a change in the GRS spectrum, a 20-fold increase in the fluorescence intensity, and a decrease in the duration of fluorescence decay.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Structural Profile Matrices for Predicting Structural Properties of Proteins
    (World Scientific Publ Co Pte Ltd, 2020-07-10) Azginoglu, Nuh; Aydin, Zafer; Celik, Mete
    Predicting structural properties of proteins plays a key role in predicting the 3D structure of proteins. In this study, new structural profile matrices (SPM) are developed for protein secondary structure, solvent accessibility and torsion angle class predictions, which could be used as input to 3D prediction algorithms. The structural templates employed in computing SPMs are detected by eight alignment methods in LOMETS server, gap affine alignment method, ScanProsite, PfamScan, and HHblits. The contribution of each template is weighted by its similarity to target, which is assessed by several sequence alignment scores. For comparison, the SPMs are also computed using Homolpro, which uses BLAST for target template alignments and does not assign weights to templates. Incorporating the SPMs into DSPRED classifier, the prediction accuracy improves significantly as demonstrated by cross-validation experiments on two difficult benchmarks. The most accurate predictions are obtained using the SPMs derived by threading methods in LOMETS server. On the other hand, the computational cost of computing these SPMs was the highest.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 2
    Protocol for Determining the Average Speed and Frequency of Kinesin and Dynein-Driven Intraflagellar Transport (IFT) in C. Elegans
    (Elsevier, 2022-09) Turan, Merve G.; Kantarci, Hanife; Temtek, Sadiye D.; Cakici, Onur; Cevik, Sebiha; Kaplan, Oktay, I
    Here, we present a protocol to image a fluorescent-labeled intraflagellar trans-port (IFT) component in Caenorhabditis elegans with fluorescence microscopy, including steps of sample preparations, in vivo live-cell imaging, and post -micro-scopy analysis with kymographs. This protocol breaks down all processes into three categories: (1) pre-imaging preparations, (2) preparations for the time of image acquisition, and (3) post-imaging analyses. The protocol can be applied to determine the speed and frequency of moving particles. For complete details on the use and execution of this protocol, please refer to Cevik et al. (2021).
  • Article
    Citation - WoS: 4
    Citation - Scopus: 4
    Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells
    (Elsevier, 2022-12) Ayaz-Guner, Serife; Acar, Mustafa Burak; Boyvat, Dudu; Guner, Huseyin; Bozalan, Habibe; Guzel, Melis; Ozcan, Servet
    Analysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnet-ically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, fol-lowed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.
  • Editorial
    Citation - WoS: 3
    Citation - Scopus: 4
    Precision Medicine in Oncology: Challenges, Stakes and New Paradigms
    (John Libbey Eurotext Ltd, 2019-02) Cox, Stephanie; Rousseau-Tsangaris, Marina; Abou-Zeid, Nancy; Dalle, Stephane; Leurent, Pierre; Cutivet, Arnaud; Denefle, Patrice
  • Article
    Citation - WoS: 6
    Citation - Scopus: 6
    Plasmon Enhanced Emission of Perovskite Quantum Dot Films
    (Cambridge Univ Press, 2018-01-09) Dadi, Seyma; Altintas, Yemliha; Beskazak, Emre; Mutlugun, Evren; Dadl, Seyma; Altlntas, Yemliha
    We propose and demonstrate the photoluminescence enhancement of CsPbBr3 perovskite quantum dot films in the presence of Au nanoparticles. Embedded into a polymer matrix, Au nanoparticle-quantum dot film assemble prepared by an easy spin coating method enabled the photoluminescence enhancement of perovskite quantum dot films up to 78%. The properties of the synthesized perovskite QDs and gold nanoparticles have been analysed using high resolution transmission electron microscopy, X-ray diffraction, energy dispersive X-ray spectroscopy, UV-Vis absorption spectrophotometer, steady state and time-resolved photoluminescence spectrometer.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Pericardial Fluid and Vascular Tissue Engineering: A Preliminary Study
    (Ios Press, 2021-03-23) Sonmezer, Dilek; Latifoglu, Fatma; Toprak, Guler; Duzler, Ayhan; Isoglu, Ismail Alper
    BACKGROUND: The heart is surrounded by a membrane called pericardium or pericardial cavity. OBJECTIVE: In this study, we investigated the pericardial fluid (PF) for coating polycaprolactone (PCL) scaffolds. PFS, which is a PF component, was used for the coating material. In addition to using PFS for surface coating, MED and fetal bovine serum (FBS) were also used for comparison. METHODS: Pericardial fluid cells (PFSc) isolated from PF were cultured on coated PCL scaffolds for 1, 3, and 5 days. Cell viability was determined using 3-(4, 5-di-methylthiazol- 2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. RESULTS: The MTT assay results showed that the viability of cells on PCL scaffold coated with PFS increased over time (P < 0.005), and cell viability was significantly different between PCL scaffolds coated with PFS and non-coated PCL scaffolds. However, cell viability was significantly higher in the PCL scaffolds coated with PFS than non-coated and coated with FBS, MED, and PCL scaffolds. Scanning electron microscopy (SEM) microscopy images and MTT assay indicated that PFSc are attached, proliferated, and spread on PCL scaffolds, especially on PCL scaffolds coated with PFS. CONCLUSIONS: These results suggest that PFS is a biocompatible material for surface modification of PCL scaffolds, which can be used as a suitable material for tissue engineering applications.
  • Article
    Performance Analysis of Photonic Lantern Based Coherent Receivers
    (Natl Inst Optoelectronics, 2018) Oran, A.; Ozdur, I.
    In this paper, we present the simulation results for bit-error-rate improvements of photonic lantern based coherent LIDAR systems. Our results show that using a 19-port photonic lantern, the bit-error-rate can be improved to 0.06 from 0.30 for a range of 100 meters, corresponds to a detection rate improvement from 70% to 94%.