Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 2Citation - Scopus: 2Fabrication of Bioactive Helix Aspersa Extract-Loaded Chitosan-Based Bilayer Wound Dressings for Skin Tissue Regeneration(Amer Chemical Soc, 2024) Perpelek, Merve; Tıhmınlıoğlu, Funda; Tamburaci, Sedef; Karakasli, Ahmet; Tihminlioglu, FundaIn recent years, there has been a notable shift toward exploring plant and animal extracts for the fabrication of tissue engineering structures that seamlessly integrate with the human body, providing both biological compatibility and physical reinforcement. In this particular investigation, we synthesized bilayer wound dressings by incorporating snail (Helix aspersa) secretions, comprising mucus and slime, into chitosan matrices via lyophilization and electrospinning methodologies. A nanofiber layer was integrated on top of the porous structure to mimic the epidermal layer for keratinocyte activity as well as acting as an antibacterial barrier against possible infection, whereas a porous structure was designed to mimic the dermal microenvironment for fibroblast activity. Comprehensive assessments encompassing physical characterization, antimicrobial efficacy, in vitro bioactivity, and wound healing potential were conducted on these bilayer dressings. Our findings revealed that the mucus and slime extract loading significantly altered the morphology in terms of nanofiber diameter and average pore size. Snail extracts loaded on a nanofiber layer of bilayer dressings showed slight antimicrobial activity against Staphylococcus epidermidis and Escherichia coli. An in vitro release study of slime extract loaded in the nanofiber layer indicated that both groups 1 and 2 showed a burst release up to 6 h, and a sustained release was observed up to 96 h for group 1, whereas slime extract release from group 2 continued up to 72 h. In vitro bioactivity assays unveiled the favorable impact of mucus and slime extracts on NIH/3T3 fibroblast and HS2 keratinocyte cell attachment, proliferation, and glycosaminoglycan synthesis. Furthermore, our investigations utilizing the in vitro scratch assay showcased the proliferative and migratory effects of mucus and slime extracts on skin cells. Collectively, our results underscore the promising prospects of bioactive snail secretion-loaded chitosan constructs for facilitating skin regeneration and advancing wound healing therapies.Article Citation - WoS: 1Comparison of Cell-Penetrating and Fusogenic Tat-Ha2 Peptide Performance in Peptideplex, Multicomponent, and Conjugate Sirna Delivery Systems(Amer Chemical Soc, 2024) Uz, Metin; Bulmus, Volga; Altinkaya, Sacide AlsoyIn this study, the performance of the cell-penetrating and fusogenic peptide, TAT-HA2, which consists of a cell-permeable HIV trans-activator of transcription (TAT) protein transduction domain and a pH-responsive influenza A virus hemagglutinin protein (HA2) domain, was comparatively evaluated for the first time in peptideplex, multicomponent, and conjugate siRNA delivery systems. TAT-HA2 in all three systems protected siRNA from degradation, except in the conjugate system with a low Peptide/siRNA ratio. The synergistic effect of different peptide domains enhanced the transfection efficiency of multicomponent and conjugate systems compared to that of peptideplexes, which was attributed to the surface configuration of TAT-HA2 peptides depending on the nature of attachment. Particularly, the multicomponent system showed better cellular uptake and endosomal escape than the peptideplexes, resulting in enhanced siRNA delivery in the cytoplasm. In addition, the presence of cleavable disulfide bonds in multicomponent and conjugate systems promoted the effective siRNA delivery in the cytoplasm, resulting in improved gene silencing activity. The multicomponent system reduced the level of luciferase expression in SKOV3 cells to 45% (+/- 4). In contrast, the conjugate system and the commercially available siRNA transfection agent, Lipofectamine RNAiMax, caused luciferase suppression down to 55% (+/- 2) at a siRNA dose of 100 nM. For the same dose, the peptideplex system could only reduce the luciferase expression to 65% (+/- 5). None of the developed systems showed significant toxicity at any dose. Overall, the TAT-HA2 peptide is promising as a siRNA delivery vector; however, its performance depends on the nature of attachment and, as a result, its surface configuration on the developed delivery system.Article Citation - WoS: 5Citation - Scopus: 5Light-Induced, Liquid Crystal-Templated Fabrication of Large-Area Pure Nanoporous Gold Films With High-Density Plasmonic Cavities(Amer Chemical Soc, 2024) Orhan, Ozan Baran; Polat, Nahit; Demir, Seren; Balci, Fadime Mert; Balci, SinanNanoporous gold (NPG) films are three-dimensional gold (Au) frameworks characterized by a uniform distribution of nanoscale irregular pores. Typically produced via a dealloying process, where the less noble silver (Ag) is selectively etched out, NPG films offer a large surface area, excellent chemical stability, remarkable catalytic activity, unique optical properties, and biocompatibility. These attributes make them invaluable for applications in catalysis, plasmonics, biosensors, and nanophotonics. However, the presence of residual Ag from the dealloying process can limit their performance in certain applications. In this study, we report a novel method for the fabrication of ultrapure, large-area NPG films (several cm2) using a light-induced and liquid crystal-templated method. A hexagonal lyotropic liquid crystal containing a strong acid and a nonionic surfactant is combined with an aqueous solution of HAuCl4, followed by the photochemical synthesis of gold nanoparticles (NPs) within the liquid crystal. After calcination of the Au NP-containing liquid crystal film at high temperature, pure NPG films are produced. We demonstrate surface-enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) molecules adsorbed on the NPG films and detect extremely low concentrations (below 10-6 M) of R6G. Additionally, we thoroughly investigated the formation and optical properties of the NPG films. The results reveal that the ultrapure NPG films contain high-density plasmonic nanocavities, where substantial electromagnetic fields are generated, leading to significant enhancement of optical processes at nanoscale dimensions.Article Citation - WoS: 4Citation - Scopus: 4Organolabeler: a Quick and Accurate Annotation Tool for Organoid Images(Amer Chemical Soc, 2024) Kahveci, Burak; Polatli, Elifsu; Bastanlar, Yalin; Guven, SinanOrganoids are self-assembled 3D cellular structures that resemble organs structurally and functionally, providing in vitro platforms for molecular and therapeutic studies. Generation of organoids from human cells often requires long and costly procedures with arguably low efficiency. Prediction and selection of cellular aggregates that result in healthy and functional organoids can be achieved by using artificial intelligence-based tools. Transforming images of 3D cellular constructs into digitally processable data sets for training deep learning models requires labeling of morphological boundaries, which often is performed manually. Here, we report an application named OrganoLabeler, which can create large image-based data sets in a consistent, reliable, fast, and user-friendly manner. OrganoLabeler can create segmented versions of images with combinations of contrast adjusting, K-means clustering, CLAHE, binary, and Otsu thresholding methods. We created embryoid body and brain organoid data sets, of which segmented images were manually created by human researchers and compared with OrganoLabeler. Validation is performed by training U-Net models, which are deep learning models specialized in image segmentation. U-Net models, which are trained with images segmented by OrganoLabeler, achieved similar or better segmentation accuracies than the ones trained with manually labeled reference images. OrganoLabeler can replace manual labeling, providing faster and more accurate results for organoid research free of charge.Article Citation - WoS: 11Citation - Scopus: 11Quantitative Evaluation of the Pore and Window Sizes of Tissue Engineering Scaffolds on Scanning Electron Microscope Images Using Deep Learning(Amer Chemical Soc, 2024) Karaca, Ilayda; Dikici, Betul AldemirThe morphological characteristics of tissue engineering scaffolds, such as pore and window diameters, are crucial, as they directly impact cell-material interactions, attachment, spreading, infiltration of the cells, degradation rate and the mechanical properties of the scaffolds. Scanning electron microscopy (SEM) is one of the most commonly used techniques for characterizing the microarchitecture of tissue engineering scaffolds due to its advantages, such as being easily accessible and having a short examination time. However, SEM images provide qualitative data that need to be manually measured using software such as ImageJ to quantify the morphological features of the scaffolds. As it is not practical to measure each pore/window in the SEM images as it requires extensive time and effort, only the number of pores/windows is measured and assumed to represent the whole sample, which may cause user bias. Additionally, depending on the number of samples and groups, a study may require measuring thousands of samples and the human error rate may increase. To overcome such problems, in this study, a deep learning model (Pore D2) was developed to quantify the morphological features (such as the pore size and window size) of the open-porous scaffolds automatically for the first time. The developed algorithm was tested on emulsion-templated scaffolds fabricated under different fabrication conditions, such as changing mixing speed, temperature, and surfactant concentration, which resulted in scaffolds with various morphologies. Along with the developed model, blind manual measurements were taken, and the results showed that the developed tool is capable of quantifying pore and window sizes with a high accuracy. Quantifying the morphological features of scaffolds fabricated under different circumstances and controlling these features enable us to engineer tissue engineering scaffolds precisely for specific applications. Pore D2, an open-source software, is available for everyone at the following link: https://github.com/ilaydakaraca/PoreD2.Article Citation - WoS: 4Citation - Scopus: 4Anisotropic Single-Layer Tilted Α-Bi: Identification of Uniaxial Strain Via Raman Spectrum(Amer Chemical Soc, 2024) Dogan, Kadir Can; Yagmurcukardes, MehmetIn the present study, the structural, vibrational, electronic, and elastic properties of single-layer alpha-Bi are investigated by performing density functional theory-based first-principles calculations. Structural optimizations show that free-standing alpha-Bi possesses a tilted black phosphorus-like anisotropic structure. The phonon band dispersions and linear-elastic parameters reveal the dynamical and mechanical stability of the alpha-Bi structure, respectively. In addition, quantum molecular dynamics simulations indicate the thermal stability of the single layer at room temperature. Electronically, it is found that alpha-Bi exhibits an indirect band gap semiconducting behavior, whose hole and electron effective masses are shown to be orientation-dependent with the latter being more anisotropic. Such anisotropic effective masses reveal orientation-dependent transport properties in single-layer alpha-Bi. Moreover, the orientation-dependent elastic features of alpha-Bi show that at an angle of 45 degrees with respect to the zigzag (ZZ) orientation, an auxetic behavior is predicted for the structure. Furthermore, the impact of uniaxial strains along the two main orientations (ZZ and armchair directions) is investigated on the vibrational properties of single-layer alpha-Bi. The phononic stability of the structure is first predicted at the strain limits (+/- 5) for both directions, and the results reveal the preserved stability of the single layer under both compressive and tensile strains. The calculated Raman spectra under uniaxial strains show that the type (compressive or tensile) and the direction of the applied strain can be deduced from the Raman spectra analysis. Overall, strain-induced modifications in the Raman spectrum of 2D alpha-Bi in terms of the peak positions may be useful tools for the characterization of induced strain in experimental studies.Article Citation - WoS: 10Citation - Scopus: 9Exploring Neuronal Differentiation Profiles in Sh-Sy5y Cells Through Magnetic Levitation Analysis(Amer Chemical Soc, 2024) Kartal, Rumeysa Bilginer; Yildiz, Ahu ArslanMagnetic levitation (MagLev) is a powerful and versatile technique that can sort objects based on their density differences. This paper reports the sorting of SH-SY5Y cells for neuronal differentiation by the MagLev technique. Herein, SH-SY5Y cells were differentiated with retinoic acid (RA) and brain-derived neurotrophic factor (BDNF). Neuronal differentiation was confirmed by neurite extension measurement and the immunostaining assay. Neurites reached the maximum length on day 9 after sequential treatment with RA-BDNF. Neuronal marker expression of un-/differentiated cells was investigated by beta-III tubulin and neuronal nuclei (NeuN) and differentiated cells exhibited a higher fluorescence intensity compared to un-/differentiated cells. MagLev results revealed that the density of differentiated SH-SY5Y cells gradually increased from 1.04 to 1.06 g/mL, while it remained stable at 1.05 g/mL for un-/differentiated cells. These findings signified that cell density would be a potent indicator of neuronal differentiation. Overall, it was shown that MagLev methodology can provide rapid, label-free, and easy sorting to analyze the differentiation of cells at a single-cell level.Article Citation - WoS: 6Citation - Scopus: 6Ion and Molecule Sieving Through Highly Stable Graphene-Based Laminar Membranes(Amer Chemical Soc, 2023) Yuan, Gang; Jiang, Yu; Wang, Xiao; Ma, Jiaojiao; Ma, Hao; Wang, Xiang; Hu, ShengBiological ion channels use both their sizes and residual groups to reject large ions and molecules and allow highly selective permeation of small species with similar sizes. To realize these properties in artificial membranes, the main challenge is the precise control of both the channel size and the interior at the nanoscale. Here we report the permeation of ions and molecules through interlayer channels in graphene-based laminar membranes. The amino groups decorated on channel walls are found to form hydrogen bond networks with intercalated water molecules, thus providing a highly stable laminate structure and a controlled channel size. Solutes with hydration diameters of >10 angstrom are precisely sieved out. Small species permeate through with selectivities of up to a few thousand, governed by their distinct electrical interactions with channels depending on the atomistic distance from the charged species to the channel walls. Our work offers important insights into manipulating channel structures for enhanced separation performance at the nanoscale.