PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Editorial Editorial: Advancing Biotechnology in Turkiye: a Dedication To All Women(Springer, 2025) Cadirci, Bilge Hilal; Buyukkileci, Ali Oguz; Binay, BarisArticle Citation - WoS: 1Citation - Scopus: 1Imbalance in Redox Homeostasis Is Associated With Neurodegeneration in the Murine Model of Tay-Sachs Disease(Springer, 2025) Basirli, Hande; Ates, Nurselin; Seyrantepe, VolkanBackgroundTay-Sachs disease is a neurodegenerative disorder characterized by a build-up of GM2 ganglioside in the brain, which results in progressive central nervous system dysfunction. Our group recently generated Hexa-/-Neu3-/- mice, a murine model with neuropathological abnormalities similar to the infantile form of Tay-Sachs disease. Previously, we reported progressive neurodegeneration with neuronal loss in the brain sections of Hexa-/-Neu3-/- mice. However, the relationship between the severity of neurodegeneration and the imbalance in redox homeostasis was not yet clarified in Hexa-/-Neu3-/- mice. Here, we evaluated whether neurodegeneration is associated with oxidative stress in the tissues and cells of Hexa-/-Neu3-/- mice and neuroglia cells from Tay-Sachs patients.Methods and resultsCell death and oxidative stress-related markers were evaluated in four brain regions and fibroblasts of 5-month-old WT, Hexa-/-, Neu3-/-, and Hexa-/-Neu3-/- mice and human neuroglia cells using Western blot, RT-PCR, and immunohistochemistry analyses. We further analyzed oxidative stress levels in the samples using flow cytometry analyses. We discovered neuronal death, alterations in intracellular ROS levels, and damaging effects of oxidative stress, especially in the cerebellum and fibroblasts of Hexa-/-Neu3-/- mice.ConclusionsOur results showed that alteration in redox homeostasis might be related to neurodegeneration in the murine model of Tay-Sachs Disease. These findings suggest that targeting the altered redox balance and increased oxidative stress might be a rational therapeutic approach for alleviating neurodegeneration and treating Tay-Sachs disease.Article Citation - WoS: 5Citation - Scopus: 5Differences and Similarities in Biophysical and Biological Characteristics Between U87 Mg Glioblastoma and Astrocyte Cells(Springer, 2023) Özdil, Berrin; Çalık Kocatürk, Duygu; Altunayar Ünsalan, Çisem; Açıkgöz, Eda; Oltulu, Fatih; Görgülü, Volkan; Uysal, Ayşegül; Öktem, Gülperi; Ünsalan, Ozan; Güler, Günnur; Aktuğ, HüseyinCurrent cancer studies focus on molecular-targeting diagnostics and interactions with surroundings; however, there are still gaps in characterization based on topological differences and elemental composition. Glioblastoma (GBM cells; GBMCs) is an astrocytic aggressive brain tumor. At the molecular level, GBMCs and astrocytes may differ, and cell elemental/topological analysis is critical for identifying potential new cancer targets. Here, we used U87 MG cells for GBMCS. U87 MG cell lines, which are frequently used in glioblastoma research, are an important tool for studying the various features and underlying mechanisms of this aggressive brain tumor. For the first time, atomic force microscopy (AFM), scanning electron microscopy (SEM) accompanied by energy-dispersive X-ray spectroscopy (EDS), and X-ray photoelectron spectroscopy (XPS) are used to report the topology and chemistry of cancer (U87 MG) and healthy (SVG p12) cells. In addition, F-actin staining and cytoskeleton-based gene expression analyses were performed. The degree of gene expression for genes related to the cytoskeleton was similar; however, the intensity of F-actin, anisotropy values, and invasion-related genes were different. Morphologically, GBMCs were longer and narrower while astrocytes were shorter and more disseminated based on AFM. Furthermore, the roughness values of these cells differed slightly between the two call types. In contrast to the rougher astrocyte surfaces in the lamellipodial area, SEM-EDS analysis showed that elongated GBMCs displayed filopodial protrusions. Our investigation provides considerable further insight into rapid cancer cell characterization in terms of a combinatorial spectroscopic and microscopic approach.Article Citation - WoS: 7Citation - Scopus: 6Visceral Leishmaniasis Caused by Leishmania Tropica(Springer, 2023) Özbilgin, Ahmet; Tunalı, Varol; Çavuş, İbrahim; Vardarlı Tetik, Aslı; Dinç, Melike; Yalçın, Talat; Gündüz, Cumhur; Beyaz, Merve; Köse, ŞükranPurposeIn Turkey, the main causative agent of visceral leishmaniasis (VL) is Leishmania. infantum and the main causative agent of cutaneous leishmaniasis (CL) is Leishmania tropica. In this study, we aimed to discuss the possible mechanisms, clinical aspects, and threat of visceralizing L. tropica.MethodsThis study includes seven cases of VL caused by L. tropica.Five patients were male (71%) and four were adults (57%).ResultsAll the VL patients complained of fever and splenomegaly. Fatigue, pancytopenia, and hepatomegaly were present in six patients each (86%), while weight loss and gastrointestinal system (GIS) symptoms were present in 5 patients (71%).ConclusionsIn this study, we have evaluated seven cases of visceralized L. tropica (VLT) in the context of the changing leishmaniasis epidemiology in Turkey. We have evaluated the possible mechanisms of visceralization; inter- and intraspecies genetic exchange with all the old world leishmaniasis agents present in the region, stress induced by inappropriate use of drugs, and possible ongoing adaptation mechanisms of Leishmania spp. The threat posed by VLT is significant as L. tropica is the most widespread and most common cause of leishmaniasis in Turkey. We do not know the vectorial capacity of the sand flies for the transmission of VLT strains or if these strains are in circulation in Turkey. Future studies should be carried out to investigate these issues as the transition of L. tropica from a mild disease-causing agent to a mortal one poses a significant public health concern for Turkey and Europe.Article Citation - WoS: 4Citation - Scopus: 4Mapping of Quantitative Trait Loci for the Nutritional Value of Fresh Market Tomato(Springer, 2023) Gürbüz Çolak, Nergiz; Tek Eken, Neslihan; Ülger, Mehmet; Frary, Anne; Doğanlar, SamiThe incidence of many diseases, such as cancer, cardiovascular diseases, and diabetes, is associated with malnutrition and an unbalanced daily diet. Vegetables are an important source of vitamins and essential compounds for human health. As a result, such metabolites have increasingly become the focus of breeding programs. Tomato is one of the most popular components of our daily diet. Therefore, the improvement of tomato's nutritional quality is an important goal. In the present study, we performed targeted metabolic profiling of an interspecific Solanum pimpinellifolium x S. lycopersicum inbred backcross line (IBL) population and identified quantitative trait loci responsible for the nutritional value of tomato. Transgressive segregation was apparent for many of the nutritional compounds such that some IBLs had extremely high levels of various amino acids and vitamins compared to their parents. A total of 117 QTLs for nutritional traits including 62 QTLs for amino acids, 18 QTLs for fatty acids, 12 QTLs for water-soluble vitamins, and 25 QTLs for fat-soluble vitamins were identified. Moreover, almost 24% of identified QTLs were confirmed in previous studies, and 40 possible gene candidates were found for 18 identified QTLs. These findings can help breeders to improve the nutritional value of tomato.Article Citation - WoS: 6Citation - Scopus: 6Diagnosis of Ruminant Viral Diseases With Loop-Mediated Isothermal Amplification(Springer, 2023) Ayaz Kök, Sanem; Üstün, Selcen; Taşkent, HümeyraInfectious diseases in livestock industry are major problems for animal health, food safety, and the economy. Zoonotic diseases from farm animals are significant threat to human population as well. These are notifiable diseases listed by the World Organization for Animal Health (OIE). Rapid diagnostic methods can help keep infectious diseases under control in herds. Loop-mediated isothermal amplification (LAMP) is a simple and rapid nucleic acid amplification method that is studied widely for detection of many infectious diseases in the field. LAMP allows biosensing of target DNA or RNA under isothermal conditions with high specificity in a short period of time. An untrained user can analyze results based on color change or turbidity. Here we review LAMP assays to diagnose OIE notifiable ruminant viral diseases in literature highlighting properties of LAMP method considering what is expected from an efficient, field usable diagnostic test.Article Citation - WoS: 2Citation - Scopus: 2Tuning the Solid Phase Fluorescence Emission From Long Wavelength Visible To Near-Infrared in Oxazol-5 Derivatives: Structure–property Relationship, Theoretical and Experimental Studies(Springer, 2023) Nazlı, İbrahim Hanif; Yakalı, Gül; Topkaya, Derya; İzmirli, Merve; Uzun, Sema Demirci; Alp, SerapMost of the fluorescent molecules among organic π-conjugated materials show blue or green emission in the solid phase but few of them emit red-shifted visible and near-infrared light in the material science. To create molecules emitting for this feature, two π-conjugated oxazol-5-one derivatives containing donor (OCH3) and acceptor groups (NO2) were synthesized. Their optical and charge-transport properties were investigated through experimental and theoretical methods including the single crystal X-ray crystallography, Hirshfeld Surface Analysis, photophysical studies and Density Functional Theory (DFT), respectively. In addition, FT-IR, 1H-NMR, 13C-NMR spectroscopy, cyclic voltammetry (CV) measurements were performed. According to our results, both molecules may provide the significant pathway of development of long wavelength visible and red emissive features in solid phase with the aggregation induced enhanced emission (AIEE) properties particularly in the fields of OLEDs, optical communication, defence and bioimaging.Article Citation - WoS: 3Citation - Scopus: 3Gras-Di Snp-Based Molecular Characterization and Fingerprinting of a Turkish Corylus Avellana Core Set Provide Insights Into the Cultivation and Breeding of Hazelnut in Turkey(Springer, 2023) Yanar, Ertuğrul Gazi; Doğanlar, Sami; Frary, AnneHazelnut (Corylus avellana L.) is an economically and socially important product for Turkey, the country that leads global production of this crop. The preservation of Turkish hazelnut genetic diversity and informed breeding of new cultivars are crucial for maintaining quality and crop yield stability. In this study, genotyping by random amplicon sequencing (GRAS-Di) was used to identify single-nucleotide polymorphisms (SNPs) in a panel of 96 individuals representing the Turkish national hazelnut collection. The resulting 7609 high-quality SNPs were physically mapped to the Tombul cultivar reference genome and used for population structure and diversity analyses. These analyses revealed that cultivars are not less diverse than wild accessions and that 44% of the panel had admixed ancestry. The results also indicated that recently released Turkish cultivars are highly similar to each other, suggesting that diversity analysis is an important tool that should be employed to prevent future genetic bottlenecks in this crop. A minimal marker algorithm was used to select a set of seven SNP markers that were capable of differentiating the panel accessions. These fingerprinting markers should be useful for the propagation of true-to-type elite cultivars that can be used to renew Turkey's aging hazelnut orchards.Article Citation - WoS: 5Citation - Scopus: 5The Designing of a Gel Formulation With Chitosan Polymer Using Liposomes as Nanocarriers of Amphotericin B for a Non-Invasive Treatment Model of Cutaneous Leishmaniasis(Springer, 2022) Gürbüz, Nergiz; Çetin Uyanıkgil, Emel Öykü; Özbel, Yusuf; Töz, SerayPurpose Leishmaniasis is a disease caused by different Leishmania spp., which are transmitted to humans by a bite of infected female sand flies. Cutaneous leishmaniasis (CL, oriental sore), visceral leishmaniasis (VL), and mucocutaneous leishmaniasis (MCL) are three main clinical forms, however, only CL and VL are seen in Turkey. Cutaneous leishmaniasis is characterized by skin lesion(s) and is one of the most important vector-borne diseases in Turkey with over 2000 cases reported annually in 40 out of 81 provinces. The treatment is usually made invasively and painfully by intralesional injection of pentavalent antimony compounds. Non-invasive and innovative treatment methods are needed as aimed in this study. Methods In the present study, one of the classical antileishmanial drugs, amphotericin B (AmB), encapsulated in liposomes was evaluated using non-invasive design based on chitosan, which is a nontoxic, biocompatible and biodegradable polymer. To avoid the invasive effect of conventional intralesional needle application, the drug was encapsulated in liposomes and incorporated into a chitosan gel for applying topically on the skin lesion. The efficacy of encapsulation of amphotericin B into liposomes and the drug release from liposomes were studied. The chitosan gel was evaluated for viscosity, flowability, appearance and pH. The efficacy of the drug embedded into chitosan gel, liposomal AmB alone and chitosan gel alone in four different concentrations was also tested using Leishmania spp. promastigotes in vitro. Results The findings have shown that AmB was encapsulated into the liposomes with high efficiency (86.6%) and long-term physical and chemical stability. Therefore, designed liposomal formulation was suitable for sustained release. The appearance of the drug-embedded chitosan gel was transparent and appropriate. Chitosan gels showed non- Newtonian behavior and plastic flow. The liposomal AmB also showed higher efficacy with no parasites in all concentrations while drug embedded into chitosan gel and chitosan gel alone were effective in two higher concentrations. The lower efficacy of the drug-embedded chitosan gel in 24 h in in-vitro study was probably due to slow release of the drug. Conclusion The gel design created in this study will provide ease of use for the lesions of CL patients that do not have a specific number, size, and shape. Follow-up studies by the ex-vivo macrophage infection model with Leishmania intracellular amastigote forms and Leishmania-infected animal models are needed to understand the present design's efficacy better.Article Citation - WoS: 6Citation - Scopus: 5Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk(Springer, 2021) Kıbrıs, Erman; Nalıncı Barbak, Nehir; Elmacı Irmak, NuranIn the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.