PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Development and Characterization of Starch-Fatty Acid Complexes Produced with Buckwheat Starch and Capric/Stearic Acid Using Different Reaction Conditions(Elsevier, 2025-12) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, KevserThe aim of present study was to investigate the impact of reaction parameters on the complex formation between buckwheat starch and capric acid (B-Capric) or stearic acid (B-Stearic). The most effective parameters on complex formation indicator (Complex index (CI) value) were found as reaction temperature (60-90 degrees C) and pH (5-8). Additionally, the effect of these parameters on physicochemical, pasting, and in-vitro digestibility properties of complex samples were evaluated. XRD and FTIR was also used in characterize the complex samples. In general, increasing pH increased the CI values of B-Stearic samples while decreasing those of B-Capric samples. Syneresis of buckwheat starch increased after complexation while paste clarity and swelling power diminished. The pasting properties of native starch significantly changed after complex formation. The FTIR results showed that starch structure changed with complex formation. XRD revealed that buckwheat starch, having an A-type pattern, converted to V-type pattern after complexation. Complex formation of buckwheat starch with capric and stearic acid significantly increased the RS content of buckwheat starch (19.01 %) by up to 36.25 % and 30.60 %, respectively. These results highlight the possibility of using buckwheat starch-capric acid/stearic acid complexes in food formulation to enhance the RS content.Article Citation - WoS: 1Citation - Scopus: 1The Impact of COVID-19 on Healthcare Utilization in Turkey(Elsevier, 2024-09) Ugur, Zeynep B.; Durak, AysenurObjectives: This study investigates the impact of the COVID-19 pandemic on healthcare utilization in Turkey. Methods: We utilized individual-level data derived from Turkish Statistical Institute 's annual surveys between 2014 and 2022 and estimated probit regression models. Results: We find that COVID-19 pandemic reduced healthcare utilization by 11.8% after taking into account a large set of background variables. Although our study finds that the elderly and those with health problems are more likely to use healthcare services under normal circumstances, the COVID-19 pandemic has caused notable drops in the healthcare utilization among the elderly (-6.5%) and those with health problems (-3.8%). Although those without health insurance had lower utilization of healthcare services before the pandemic, during the pandemic they were not particularly hit. Conclusion: We conclude that the pandemic did not lower the healthcare utilization in Turkey because of the supply constraints. Also, the evidence points to the reduced demand due to the fear of contagion rather than financial concerns.Article Citation - WoS: 16Citation - Scopus: 15Role of AHR, NF-kB and CYP1A1 Crosstalk With the X Protein of Hepatitis B Virus in Hepatocellular Carcinoma Cells(Elsevier, 2023-02) Celik-Turgut, Gurbet; Olmez, Nazmiye; Koc, Tugba; Ozgun-Acar, Ozden; Semiz, Asli; Dodurga, Yavuz; Sen, AlaattinIn this study, it was aimed to elucidate the interaction between aryl hydrocarbon receptor (AHR), nuclear factor -kappa B (NF-kB), and cytochrome P4501A1 (CYP1A1) with hepatitis B virus X protein (HBX) in a human liver cancer cell line (HepG2) transfected with HBX. First, AHR, NF-kB, and CYP1A1 genes were cloned into the appropriate region of the CheckMate mammalian two-hybrid recipient plasmids using a flexi vector system. Renilla and firefly luciferases were quantified using the dual-luciferase reporter assay system to measure the interactions. Secondly, transient transfections of CYP1A1 and NF-kB (RelA) were performed into HBX-positive and HBX-negative HepG2 cells. The mRNA expression of CYP1A1 and NF-kB genes were confirmed with RT-PCR, and cell viability was measured by WST-1. Further verification was assessed by measuring the activity and protein level of CYP1A1. Additionally, CYP1A1/HBX protein-protein interactions were performed with co-immunoprecipitation, which demonstrated no interaction. These results have clearly shown that the NF-kB and AHR genes interact with HBX without involving CYP1A1 and HBX protein-protein interactions. The present study confirms that AHR and NF-kB interaction plays a role in the HBV mechanism mediated via HBX and coordinating the carcinogenic or inflammatory responses; still, the CYP1A1 gene has no effect on this interaction.Article Citation - WoS: 1Citation - Scopus: 2Protocol 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, IHere, 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: 4Citation - Scopus: 4Protocol 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, ServetAnalysis 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.Article Citation - WoS: 25Citation - Scopus: 33Production of Buckwheat Starch-Myristic Acid Complexes and Effect of Reaction Conditions on the Physicochemical Properties, X-Ray Pattern and FT-IR Spectra(Elsevier, 2022-05) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, KevserIn this study, the effect of reaction parameters on complex index (CI%) value of complexes formed between buckwheat starch (BS) and myristic acid (MA) was investigated. The temperature (60-90 ?C) and MA to BS ratio (0.1-0.8 mmoL/g) were determined as the most effective parameters and their effect on CI% was evaluated using response surface methodology. The MA to BS ratio, temperature, and interaction between them had an influence on CI%. The CI% of BS-MA complexes increased with increasing MA ratio until a certain level of MA. Principal component analysis (PCA) was used for correlation analysis between parameters. Swelling power and paste clarity of BS decreased with complex formation while syneresis increased. Peak and final viscosity values of the BS-MA complexes were significantly lower than those of BS. FT-IR revealed the complex formation led to change in starch structure. The XRD confirmed the BS-MA complex formation but the BS-MA produced using 0.1 mmoL/ g at 60 ?C was not detected by XRD due to having low crystallinity, and expectedly, the lowest relative crystallinity value was achieved with this sample among complex samples. All results showed that the buckwheat be an alternative starch source for starch formation.Article Citation - WoS: 13Citation - Scopus: 15Prevention of Cisplatin-Induced Nephrotoxicity by Kidney-Targeted siRNA Delivery(Elsevier, 2022-11) Aydin, Erkin; Cebeci, Aysun; Lekesizcan, AycaCisplatin is a potent and widely used chemotherapy agent, however, nephrotoxicity limits its use. Many patients need to pause or withdraw from chemotherapy to prevent acute kidney injury. To prevent cisplatin damage, we designed chitosan/siRNA nanoparticleswhich are nontoxic and are readily taken up by HEK293 cells. The nanoparticles contained siRNA against cationic membrane transport (OCT1&2) and apoptosis related proteins (p53, PKC8, and gamma GT). In mice treated with cisplatin, serum creatinine levels increased from 15 to 88 mg/dL and blood urea nitrogen levels increased from 0.25 to 1.7 mg/dL, however, siRNA nanoparticles significantly limited these levels to 30 mg/dL and 0.55 mg/dL, respectively. Western and IHC analyses showed lower p53, PKC8, and gamma GT expressions in siRNA treated mice. Histomorphological evaluation revealed high-level protection of kidney proximal tubules from cisplatin damage. Protein expressions and extent of kidney protection were directly correlated with number of siRNA applications. Our results suggest that this novel approach for kidney -targeted delivery of select siRNAs may represent a promising therapy for preventing cisplatin-induced nephro-toxicity. Furthermore, this or other similarly sized nanocarriers could potentially be utilized to passively target kidneys for diagnostic, protective, or treatment purposes.Article Citation - WoS: 3Citation - Scopus: 4Prediction of Biomechanical Properties of Ex Vivo Human Femoral Cortical Bone Using Raman Spectroscopy and Machine Learning Algorithms(Elsevier, 2025-09) Unal, Mustafa; Unlu, Ramazan; Uppuganti, Sasidhar; Nyman, Jeffry S.This study applied Raman spectroscopy (RS) to ex vivo human cadaveric femoral mid-diaphysis cortical bone specimens (n = 118 donors; age range 21-101 years) to predict fracture toughness properties via machine learning (ML) models. Spectral features, together with demographic variables (age, sex) and structural parameters (cortical porosity, volumetric bone mineral density), were fed into support vector regression (SVR), extreme tree regression (ETR), extreme gradient boosting (XGB), and ensemble models to predict fracture-toughness metrics such as crack-initiation toughness (Kinit) and energy-to-fracture (J-integral). Feature selection was based on Raman-derived mineral and organic matrix parameters, such as nu 1Phosphate (PO4)/CH2-wag, nu 1PO4/ Amide I, and others, to capture the complex composition of bone. Our results indicate that ensemble models consistently outperformed individual models, with the best performance for crack initiation toughness (Kinit) prediction being achieved using the ensemble approach. This yielded a coefficient of determination (R2) of 0.623, root-mean squared error (RMSE) of 1.320, mean absolute error (MAE) of 1.015, and mean percentage absolute error (MAPE) of 0.134. For prediction of the overall energy to propagate a crack (J-integral), the XGB model achieved an R2 of 0.737, RMSE of 2.634, MAE of 2.283, and MAPE of 0.240. This study highlights the importance of incorporating mineral quality properties (MP) and organic matrix properties (OMP) for enhanced prediction accuracy. This work represents the first-ever study combining Raman spectroscopy with other clinical and structural features to predict fracture toughness of human cortical bone, demonstrating the potential of artificial intelligence (AI) and ML in advancing bone research. Future studies could focus on larger datasets and more advanced modeling techniques to further improve predictive capabilities.Article Citation - WoS: 4Citation - Scopus: 5Novel Insights Into Bacillus Thuringiensis: Beyond Its Role as a Bioinsecticide(Elsevier, 2025-03) Jouzani, Gholamreza Salehi; Sharafi, Reza; Argentel-Martinez, Leandris; Penuelas-Rubio, Ofelda; Ozkan, Ceyda; Incegul, Bengisu; Azizoglu, Ugur; Salehi Jouzani, GholamrezaThis review explores the diverse applications of Bacillus thuringiensis (Bt) beyond its traditional role as a bioinsecticide. Bt produces a variety of compounds with distinct chemical structures and biological activities. These include antimicrobial agents effective against plant pathogens and bioactive compounds that promote plant growth through the production of siderophores, hormones, and enzymes. Additionally, Bt's industrial potential is highlighted, encompassing biofuel production, bioplastics, nanoparticle synthesis, food preservation, anticancer therapies, and heavy metal bioremediation. This critical analysis emphasizes recent advancements and applications, providing insights into Bt's role in sustainable agriculture, biotechnology, and environmental management.Article Citation - WoS: 2Citation - Scopus: 2Membrane Binding and Lipid-Protein Interaction of the C2 Domain From Coagulation Factor V(Elsevier, 2024) Ohkubo, Y. Zenmei; Radulovic, Peter W.; Kahira, Albert N.; Madsen, Jesper J.Anchoring of coagulation factors to anionic regions of the membrane involves the C2 domain as a key player. The rate of enzymatic reactions of the coagulation factors is increased by several orders of magnitude upon membrane binding. However, the precise mechanisms behind the rate acceleration remain unclear, primarily because of a lack of understanding of the conformational dynamics of the C2-containing factors and corresponding complexes. We elucidate the membrane-bound form of the C2 domain from human coagulation factor V (FV-C2) by characterizing its membrane binding the specific lipid -protein interactions. Employing all-atom molecular dynamics simulations and leveraging the highly mobile membrane-mimetic (HMMM) model, we observed spontaneous binding of FV-C2 to a phosphatidylserine (PS)-containing membrane within 2-25 ns across twelve independent simulations. FV-C2 interacted with the membrane through three loops (spikes 1-3), achieving a converged, stable orientation. Multiple HMMM trajectories of the spontaneous membrane binding provided extensive sampling and ample data to examine the membrane-induced effects on the conformational dynamics of C2 as well as specific lipid -protein interactions. Despite existing crystal structures representing presumed "open" and "closed" states of FV-C2, our results revealed a continuous distribution of structures between these states, with the most populated structures differing from both "open" and "closed" states observed in crystal environments. Lastly, we characterized a putative PS-specific binding site formed by K23, Q48, and S78 located in the groove enclosed by spikes 1-3 (PS-specificity pocket), suggesting a different orientation of a bound headgroup moiety compared to previous proposals based upon analysis of static crystal structures.