Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Erratum Correction: Integrated Spectroscopic and Morphological Analyses Reveal Cellular Shifts in Gene-Silenced Melanoma CSCs (Scientific Reports, (2025), 15, 1, (31175), 10.1038/S41598-025-17155-2)(Nature Research, 2025) Özdil, B.; Güler, G.; Ataman, E.; Aktuǧ, H.Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-025-17155-2, published online 25 August 2025 The original version of this Article contained an error, where the legends of Figure 4 and Figure 5 were erroneously added in the Materials and methods section, under the subheading ‘Statistical analysis’. The duplicate legends have now been removed from the body of the text. The original Article has been corrected. © 2025 Elsevier B.V., All rights reserved.Erratum Author Correction: the Influence of Nano Filter Elements on Pressure Drop and Pollutant Elimination Efficiency in Town Border Stations(Nature Research, 2023) Heris, S.Z.; Ebadiyan, H.; Mousavi, S.B.; Nami, S.H.; Mohammadpourfard, MousaThe original version of this Article contained an error in the order of the author names, which was incorrectly given as Hamed Ebadiyan, Saeed Zeinali Heris, Seyed Borhan Mousavi, Shamin Hosseini Nami & Mousa Mohammadpourfard. Consequently, in the Author Contributions section, “H.E. Investigation. S.Z.H. Supervision, Conceptualization, Methodology, Validation. S.B.M. Formal analysis, Writing original draft. S.H.N. Formal analysis, Writing original draft. M.M. Validation.” now reads: “S.Z.H. Supervision, Conceptualization, Methodology, Validation. H.E. Investigation. S.B.M. Formal analysis, Writing original draft. S.H.N. Formal analysis, Writing original draft. M.M. Validation.” The original Article has been corrected. © 2023, The Author(s).Article Citation - WoS: 6Citation - Scopus: 5Basidiomycota Species in Drosophila Gut Are Associated With Host Fat Metabolism(Nature Research, 2023) Bozkurt, Berkay; Terlemez, Gamze; Sezgin, EfeThe importance of bacterial microbiota on host metabolism and obesity risk is well documented. However, the role of fungal microbiota on host storage metabolite pools is largely unexplored. We aimed to investigate the role of microbiota on D. melanogaster fat metabolism, and examine interrelatedness between fungal and bacterial microbiota, and major metabolic pools. Fungal and bacterial microbiota profiles, fat, glycogen, and trehalose metabolic pools are measured in a context of genetic variation represented by whole genome sequenced inbred Drosophila Genetic Reference Panel (DGRP) samples. Increasing Basidiomycota, Acetobacter persici, Acetobacter pomorum, and Lactobacillus brevis levels correlated with decreasing triglyceride levels. Host genes and biological pathways, identified via genome-wide scans, associated with Basidiomycota and triglyceride levels were different suggesting the effect of Basidiomycota on fat metabolism is independent of host biological pathways that control fungal microbiota or host fat metabolism. Although triglyceride, glycogen and trehalose levels were highly correlated, microorganisms’ effect on triglyceride pool were independent of glycogen and trehalose levels. Multivariate analyses suggested positive interactions between Basidiomycota, A. persici, and L. brevis that collectively correlated negatively with fat and glycogen pools. In conclusion, fungal microbiota can be a major player in host fat metabolism. Interactions between fungal and bacterial microbiota may exert substantial control over host storage metabolite pools and influence obesity risk. © 2023, Springer Nature Limited.Article Citation - WoS: 11Citation - Scopus: 13Fli1 and Fra1 Transcription Factors Drive the Transcriptional Regulatory Networks Characterizing Muscle Invasive Bladder Cancer(Nature Research, 2023) Güneri Sözeri, Perihan Yağmur; Özden Yılmaz, Gülden; Kısım, Aslı; Çakıroğlu, Ece; Eray, Aleyna; Uzuner, Hamdiye; Karakülah, Gökhan; Pesen Okvur, Devrim; Şentürk, Şerif; Erkek Özhan, Serapis and progression of this disease. In this study, we defined the active regulatory landscape of MIBC and NMIBC cell lines using H3K27ac ChIP-seq and used an integrative approach to combine our findings with existing data. Our analysis revealed FRA1 and FLI1 as two critical transcription factors differentially regulating MIBC regulatory landscape. We show that FRA1 and FLI1 regulate the genes involved in epithelial cell migration and cell junction organization. Knock-down of FRA1 and FLI1 in MIBC revealed the downregulation of several EMT-related genes such as MAP4K4 and FLOT1. Further, ChIP-SICAP performed for FRA1 and FLI1 enabled us to infer chromatin binding partners of these transcription factors and link this information with their target genes. Finally, we show that knock-down of FRA1 and FLI1 result in significant reduction of invasion capacity of MIBC cells towards muscle microenvironment using IC-CHIP assays. Our results collectively highlight the role of these transcription factors in selection and design of targeted options for treatment of MIBC.Article Citation - WoS: 8Citation - Scopus: 9Neuroprotective Metabolites Via Fungal Biotransformation of a Novel Sapogenin, Cyclocephagenol(Nature Research, 2022) Küçüksolak, Melis; Üner, Göklem; Ballar Kırmızıbayrak, Petek; Bedir, ErdalCyclocephagenol (1), a novel cycloartane-type sapogenin with tetrahydropyran unit, is only encountered in Astragalus species. This rare sapogenin has never been a topic of biological activity or modification studies. The objectives of this study were; (i) to perform microbial transformation studies on cyclocephagenol (1) using Astragalus endophyte, Alternaria eureka 1E1BL1, followed by isolation and structural characterization of the metabolites; (ii) to investigate neuroprotective activities of the metabolites; (iii) to understand structure–activity relationships towards neuroprotection. The microbial transformation of cyclocephagenol (1) using Alternaria eureka resulted in the production of twenty-one (2–22) previously undescribed metabolites. Oxidation, monooxygenation, dehydration, methyl migration, epoxidation, and ring expansion reactions were observed on the triterpenoid skeleton. Structures of the compounds were established by 1D-, 2D-NMR, and HR-MS analyses. The neuroprotective activities of metabolites and parent compound (1) were evaluated against H2O2-induced cell injury. The structure–activity relationship (SAR) was established, and the results revealed that 1 and several other metabolites had potent neuroprotective activity. Further studies revealed that selected compounds reduced the amount of ROS and preserved the integrity of the mitochondrial membrane. This is the first report of microbial transformation of cyclocephagenol.Article Citation - WoS: 32Citation - Scopus: 31Wien Effect in Interfacial Water Dissociation Through Proton-Permeable Graphene Electrodes(Nature Research, 2022) Cai, Junhao; Griffin, Eoin; Guarochico-Moreira, Victor H.; Barry, D.; Xin, B.; Yağmurcukardeş, Mehmet; Zhang, Sheng; Geim, Andre K.; Peeters, François M.; Lozada-Hidalgo, MarceloStrong electric fields can accelerate molecular dissociation reactions. The phenomenon known as the Wien effect was previously observed using high-voltage electrolysis cells that produced fields of about 107 V m−1, sufficient to accelerate the dissociation of weakly bound molecules (e.g., organics and weak electrolytes). The observation of the Wien effect for the common case of water dissociation (H2O ⇆ H+ + OH−) has remained elusive. Here we study the dissociation of interfacial water adjacent to proton-permeable graphene electrodes and observe strong acceleration of the reaction in fields reaching above 108 V m−1. The use of graphene electrodes allows measuring the proton currents arising exclusively from the dissociation of interfacial water, while the electric field driving the reaction is monitored through the carrier density induced in graphene by the same field. The observed exponential increase in proton currents is in quantitative agreement with Onsager’s theory. Our results also demonstrate that graphene electrodes can be valuable for the investigation of various interfacial phenomena involving proton transport.Article Citation - WoS: 40Citation - Scopus: 38Gas Permeation Through Graphdiyne-Based Nanoporous Membranes(Nature Research, 2022) Zhou, Zhihua; Tan, Yongtao; Yang, Qian; Bera, Achintya; Xiong, Zecheng; Yağmurcukardeş, Mehmet; Kim, MinsooNanoporous membranes based on two dimensional materials are predicted to provide highly selective gas transport in combination with extreme permeance. Here we investigate membranes made from multilayer graphdiyne, a graphene-like crystal with a larger unit cell. Despite being nearly a hundred of nanometers thick, the membranes allow fast, Knudsen-type permeation of light gases such as helium and hydrogen whereas heavy noble gases like xenon exhibit strongly suppressed flows. Using isotope and cryogenic temperature measurements, the seemingly conflicting characteristics are explained by a high density of straight-through holes (direct porosity of ∼0.1%), in which heavy atoms are adsorbed on the walls, partially blocking Knudsen flows. Our work offers important insights into intricate transport mechanisms playing a role at nanoscale.Article Citation - WoS: 192Citation - Scopus: 194Multispectral Graphene-Based Electro-Optical Surfaces With Reversible Tunability From Visible To Microwave Wavelengths(Nature Research, 2021) Ergoktas, M. Said; Bakan, Gökhan; Kovalska, Evgeniya; Le Fevre, Lewis W.; Fields, Richard P.; Steiner, Pietro; Yu, Xiaoxiao; Balcı, SinanOptical materials with colour changing abilities have been explored for use in display devices(1), smart windows(2,3) or in the modulation of visual appearance(4-6). The efficiency of these materials, however, has strong wavelength dependence, which limits their functionality to a specific spectral range. Here, we report graphene-based electro-optical devices with unprecedented optical tunability covering the entire electromagnetic spectrum from the visible to microwave. We achieve this non-volatile and reversible tunability by electro-intercalation of lithium into graphene layers in an optically accessible device structure. The unique colour changing capability, together with area-selective intercalation, inspires the fabrication of new multispectral devices, including display devices and electro-optical camouflage coating. We anticipate that these results provide realistic approaches for programmable smart optical surfaces with a potential utility in many scientific and engineering fields such as active plasmonics and adaptive thermal management.Article Citation - WoS: 5Citation - Scopus: 3Apol1 Variant Alleles Associate With Reduced Risk for Opportunistic Infections in Hiv Infection(Nature Research, 2021) An, Ping; Sezgin, Efe; Kirk, Gregory D.; Duggal, Priya; Binns-Roemer, Elizabeth; Nelson, George; Limou, SophieApolipoprotein L1 (APOL1), an innate immune factor against African trypanosoma brucei, inhibits HIV-1 in vitro. The impact of APOL1 G1-G2 variants on HIV-1-associated opportunistic infections (OIs) is unknown. Here, we report findings from a metaanalysis of four HIV/AIDS prospective cohorts (ALIVE, LSOCA, MACS, and WIHS) including 2066 African American participants. Using a global test combining all four cohorts, carriage of two APOL1 variant alleles is associated with a 50% reduction in odds of OI (combined OR 0.50, 95% CI 0.33-0.76). Subgroup analysis of OI etiological categories (viral, parasitic, fungal and Mycobacterial) suggests the possibility of specific protection from fungal infections (OR 0.54. 95% CI 0.32-0.93; P-Bonferroni corrected=0.08). We observe an association of APOL1 variant alleles with host protection against OI in HIV-positive individuals. The study suggests a broader role of APOL1 variant alleles in innate immunity in vivo. An et al. determine the presence of variants of the innate immune factor APOL1 in four cohorts of HIV-positive patients. The study suggests that APOL1 might confer carriers of two variant alleles protection from HIV related opportunistic infections, especially fungal infections.