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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Discovery of the aminated quinoxalines as potential active molecules(Bentham Science Publishers, 2024) Bener, Sedef; Bayrak, Nilüfer; Mataracı-Kara, Emel; Yıldız, Mahmut; Sever, Belgin; Tuyun, Amaç Fatih; Department of Molecular Biology and Genetics; Çiftçi, Halil İbrahim; Department of Molecular Biology and Genetics; College of SciencesBackground: In recent years, as the biological activity of the quinoxaline skeleton has been revealed in numerous studies, interest in synthesizing new prototype molecules for the treatment of many chronic diseases, especially cancer, has increased. Methods: The desired alkoxy substituted aminoquinoxalines (AQNX1-9) were synthesized by the reaction of QNX and alkoxy substituted aryl amines such as 2-methoxyaniline, 4-methoxyaniline, 2ethoxyaniline, 3-ethoxyaniline, 4-ethoxyaniline, 4-butoxyaniline, 2,4-dimethoxyaniline, 3,4dimethoxyaniline, and 3,5-dimethoxyaniline according to the previously published procedure. QNX was aminated in DMSO at 130°C. We synthesized various alkoxy substituted aminoquinoxaline compounds (AQNX1-9) and evaluated their anticancer and antimicrobial activities in order to expand the search to related structures. In particular, two aminoquinoxaline (AQNX5 and AQNX6) compounds, coded as NSC D-835971/1 and NSC D-835972/1 by the National Cancer Institute in the USA, were screened for anticancer screening at a dose of 10-5 M on a full panel of 60 human cell lines obtained from nine human cancer cell types (leukemia, melanoma, non-small cell lung, colon, central nervous system, ovarian, kidney, prostate, and breast cancer). Results: Further in silico studies were also conducted for the compound AQNX5 (NSC D835971/1), which was found to be the most active antiproliferative agent, especially against leukemia cell lines. Molecular docking studies showed that AQNX5 interacted with Glu286 and Lys271 through hydrogen bonding and π-stacking interaction in the ATP binding region of Abl kinase, which is indicated as a potential target of leukemia. Besides, AQNX5 occupied the minor groove of the double helix of DNA via π-stacking interaction with DG-6. Conclusion: According to in silico pharmacokinetic determination, AQNX5 was endowed with drug-like properties as a potential anticancer drug candidate for future experiments. In the light of these findings, more research will focus on aminated quinoxalines' ability to precisely target leukemia cancer cell lines.Publication Metadata only 3D coffee stains(Royal Soc Chemistry, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Chemistry; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Söz, Çağla Koşak; Press, Daniel Aaron; Melikov, Rustamzhon; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Yılgör, Emel; Yılgör, İskender; Nizamoğlu, Sedat; PhD Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Electrical and Electronics Engineering; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/A; N/A; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; N/A; 24181; 130295When a liquid droplet (e.g., coffee, wine, etc.) is splattered on a surface, the droplet dries in a ring-shaped stain. This widely observed pattern in everyday life occurs due to the phenomenon known as a coffee stain (or coffee ring) effect. While the droplet dries, the capillary flow moves and deposits the particles toward the pinned edges, which shows a 2D ring-like structure. Here we demonstrate the transition from a 2D to a 3D coffee stain that has a well-defined and hollow sphere-like structure, when the substrate surface is switched from hydrophilic to superhydrophobic. The 3D stain formation starts with the evaporation of the pinned aqueous colloidal droplet placed on a superhydrophobic surface that facilitates the particle flow towards the liquid-air interface. This leads to spherical skin formation and a cavity in the droplet. Afterwards the water loss in the cavity due to pervaporation leads to bubble nucleation and growth, until complete evaporation of the solvent. In addition to the superhydrophobicity of the surface, the concentration of the solution also has a significant effect on 3D coffee stain formation. Advantageously, 3D coffee stain formation in a pendant droplet configuration enables the construction of all-protein lasers by integrating silk fibroin with fluorescent proteins. No tools, components and/or human intervention are needed after the construction process is initiated; therefore, 3D coffee-stains hold promise for building self-assembled and functional 3D constructs and devices from colloidal solutions.Publication Metadata only Identification of hub genes and key pathways between celiac and crohn's diseases via bioinformatics tools(2022) Gül, Kozalak; Köksal, Özgül Rıza; Department of Molecular Biology and Genetics; Atçeken, Nazente; PhD Student; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; N/ABackground: Chronic inflammatory diseases are the long-term response of the organism to any stimulus. Crohn's (CD) and Celiac (CeD) diseases are among chronic inflammatory diseases, and both cause chronic inflammation in the intestines. Both diseases are caused by polygenic, environmental, and lifestyle risk factors. Inflammation can perpetuate disease and cause it to become chronic. For this reason, CD and CeD that choose the intestine as the target organ may trigger each other. Although the relationship between these diseases is widely mentioned in the literature, scanty knowledge and research have been done on the immune mechanisms of these inflammatory diseases. Aim: This study aimed to determine hub genes, transcription factors-miRNAs, and protein-chemical interaction networks shared between CD and CeD. Methods: The NCBI-GEO datasets were downloaded and analyzed in GEO2R to identify differentially expressed genes (DEGs). STRING tool for Protein -Protein Interaction (PPI) and NetworkAnalyst tool were used for Gene Set Enrichment Analysis (GSEA), Transcription factor (TF) -miRNA Coregulatory Networks, and Protein-Chemical Interactions. Results and Discussion: GSE11501 and GSE3365 datasets were utilized to recognize 54 DEGs in CD, and CeD. 13 of these commonly expressed genes were defined as hub genes. GSEA has indicated that these genes are associated with immune system processes, cellular defense response, proteolysis, and apoptosis. KAT6A and SPI1 are transcription factors that direct the continuity of intestinal epithelial cells. Antirheumatic agents and Methotrexate are likely to be used to treat these diseases. Conclusions: In conclusion, we think that delayed-type hypersensitivity resulting from epitope propagation is a common immune mechanism of CD and CeD. Given the increasing prevalence of both CD and CeD in the population, it is clear that more studies are needed to understand the shared pathogenesis and overlapping immune mechanisms of these diseases.Publication Metadata only Atmospheric pressure plasma jet treatment of human hair fibers(2015) N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Birer, Özgür; Acar, Erhan; Keleş, Merve; Öngel, Cansu; Researcher; Master Student; Undergraduate Student; Undergraduate Student; Department of Molecular Biology and Genetics; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; Graduate School of Sciences and Engineering; College of Science; College of Science; N/A; N/A; N/A; N/AHuman hair fibers in virgin and dyed forms were treated with atmospheric pressure helium, helium/oxygen, argon, and argon/oxygen plasma jets at 20 W of power. The effects of 10-min plasma treatment on surface morphology and chemistry were studied by scanning electron microscopy and X-ray photoelectron spectroscopy, respectively. The plasma treatment was quite effective for removing the organic residues from the surface and creating oxidized functional groups. Helium plasma had a mild cleaning effect on the surfaces while argon/oxygen plasma had the strongest corrosive effect. Mild hydrogen peroxide treatment for the same duration had neither the cleaning nor the oxidizing power of the plasma jets. These types of plasma jets have the potential to replace peroxide treatment. The corrosive jets can be used to restore dyed hair fibers. In addition, the jets can be used to clean the surfaces of hair fibers to prepare samples for analytical investigations where the organic residues may induce problems. © 2015, Springer International Publishing AG.Publication Metadata only Design, semi-synthesis and examination of new gypsogenin derivatives against leukemia via Abl tyrosine kinase inhibition and apoptosis induction(Elsevier, 2022) Ulusoy, Nafia Gökçe; Emirdağ, Safiye; Sözer, Ece; Radwan, Mohamed O.; Aksel, Mehran; Özmen, Ali; Yayli, Nurettin; Karayıldırım, Tamer; Alankuş, Özgen; Tateishi, Hiroshi; Otsuka, Masami; Fujita, Mikako; Sever, Belgin; Bölükbaşı, Serap Şahin; Department of Molecular Biology and Genetics; Çiftçi, Halil İbrahim; Researcher; Department of Molecular Biology and Genetics; N/A; College of Sciences; N/A; N/AChronic myelogenous leukemia (CML) is characterized by Philadelphia translocation arising from Bcr-Abl fusion gene, which encodes abnormal oncoprotein showing tyrosine kinase (TK) function. Certain mutations in kinase domain, off-target effects and resistance problems of current TK inhibitors require the discovery of novel Abl TK inhibitors. For this purpose, herein, we synthesized new gypsogenin derivatives (6a-l) and evaluated their anticancer effects towards CML cells along with healthy cell line and different leukemic cells. Among these compounds, compound 6l was found as the most active anti-leukemic agent against K562 CML cells compared to imatinib exerting less cytotoxicity towards PBMCs (healthy). This compound also revealed significant anti -leukemic effects against Jurkat cell line. Besides, compound 6l enhanced apoptosis in CML cells with 52.4 % when compared with imatinib (61.8 %) and inhibited Abl TK significantly with an IC50 value of 13.04 +/- 2.48 mu M in a large panel of kinases accentuating Abl TK-mediated apoptosis of compound 6l in CML cells. Molecular docking outcomes showed that compound 6l formed mainly crucial interactions in the ATP-binding cleft of Abl TK similar to that of imatinib. Ultimately, in silico pharmacokinetic evaluation of compound 6l indicated that this compound was endowed with anti-leukemic drug candidate features.Publication Metadata only Laser emission from single, dye-doped microdroplets situated on a superhydrophobic surface(IEEE, 2007) Department of Physics; Department of Physics; Department of Physics; Department of Chemistry; N/A; Department of Physics; Department of Molecular Biology and Genetics; Sennaroğlu, Alphan; Kurt, Adnan; Kiraz, Alper; Demirel, Adem Levent; Dündar, Mehmet Ali; Kalaycıoğlu, Hamit; Doğanay, Sultan; Faculty Member; Teaching Faculty; Faculty Member; Faculty Member; Master Student; PhD Student; Undergraduated Student; Department of Chemistry; Department of Physics; Department of Molecular Biology and Genetics; College of Sciences; College of Sciences; College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; 23851; 194455; 22542; 6568; N/A; N/A; N/AOptical microcavities are attractive in developing ultralow threshold lasers which hold a great promise for applications in optical communications systems and fundamental studies in cavity quantum electrodynamics. Up to date laser emission has been observed from various different optical microcavities: Microdisks, microspheres, micropillars, photonic crystal defect microcavities, and microdroplets flying in air. Here we report the observation of laser emission from single, stationary, dye-doped microdroplets situated on a superhydrophobic surface. In contrast to the previous demonstrations on microdroplets flying in air, the technique we use allows for the analysis of laser emission from a particular microdroplet over prolonged periods.