PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
Browse
12 results
Search Results
Now showing 1 - 10 of 12
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: 3Citation - Scopus: 3Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, GülşahAlpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.Article Citation - WoS: 1Citation - Scopus: 1Exploring the Heterogeneity of Ige-Mediated Food Allergy Through Latent Class Analysis(S. Karger AG, 2022) Akarsu, Ayşegül; Öksel Karakuş, Ceyda; Ocak, Melike; Oral, Nihan; Bilgi, Eyüp; Şahiner, Ümit Murat; Soyer, Özge; Şekerel, Bülent EnisIntroduction: Food allergy (FA) is a heterogeneous disease with multiple morbidities and a huge burden for patients and healthcare systems. Variable manifestations, comorbidities (atopic dermatitis [AD], asthma, and/or allergic rhinitis [AR]), severity (anaphylaxis), and outcomes suggest the existence of different endotypes that cluster analyses may reveal. In this study, we aimed to investigate distinct subgroups among patients with FAs using data from 524 children/adolescents. Methods: 524 patients with IgE-mediated FA (353 male [67%]; median age 4.4 years [IQR:3.0-6.8]), 354 (68%) had multiple FA. The history of AD, asthma, AR, and anaphylaxis was recorded in 59.4%, 35.5%, 24.2%, and 51.2% of the patients, respectively. Latent class analysis was carried out to distinguish clinical FA phenotypes using five potential markers of allergy severity (single/multiple FA, never/inactive/current asthma and AD, AR, and anaphylaxis). Results: Three distinct phenotypes were identified: (1) multiple FA with eczema and respiratory multimorbidity (42%), (2) multiple FA with persistent eczema (34%), and (3) single FA with respiratory multimorbidity without eczema (24%). Compared with the single FA cluster, the prevalence of AD was significantly higher in multiple FA groups. Cluster 1 had the highest frequency of AR and allergic asthma, and the lowest rate of total tolerance of FA. Discussion: We put forward the hypothesis of underlying pathogenesis according to the clinical phenotypes. While skin barrier defect may play a dominant role in the pathogenesis in Cluster 2, immune dysregulation may be dominant in Cluster 3. In Cluster 1, the most severe group, a combination of both skin barrier defects and immune dysregulation may be responsible for the clinical features.Article Citation - WoS: 25Citation - Scopus: 30Fabrication of 3d Printed Poly(lactic Acid) Strut and Wet-Electrospun Cellulose Nano Fiber Reinforced Chitosan-Collagen Hydrogel Composite Scaffolds for Meniscus Tissue Engineering(SAGE Publications, 2022) Güneş, Oylum Çolpankan; Kara, Aylin; Baysan, Gizem; Hüsemoğlu, Reşit Buğra; Akokay, Pınar; Ziylan Albayrak, Aylin; Ergür, Bekir Uğur; Havitçioğlu, HasanThe main goal of the study was to produce chitosan-collagen hydrogel composite scaffolds consisting of 3D printed poly(lactic acid) (PLA) strut and nanofibrous cellulose for meniscus cartilage tissue engineering. For this purpose, first PLA strut containing microchannels was incorporated into cellulose nanofibers and then they were embedded into chitosan-collagen matrix to obtain micro- and nano-sized topographical features for better cellular activities as well as mechanical properties. All the hydrogel composite scaffolds produced by using three different concentrations of genipin (0.1, 0.3, and 0.5%) had an interconnected microporous structure with a swelling ratio of about 400% and water content values between 77 and 83% which is similar to native cartilage extracellular matrix. The compressive strength of all the hydrogel composite scaffolds was found to be similar (∼32 kPa) and suitable for cartilage tissue engineering applications. Besides, the hydrogel composite scaffold comprising 0.3% (w/v) genipin had the highest tan δ value (0.044) at a frequency of 1 Hz which is around the walking frequency of a person. According to the in vitro analysis, this hydrogel composite scaffold did not show any cytotoxic effect on the rabbit mesenchymal stem cells and enabled cells to attach, proliferate and also migrate through the inner area of the scaffold. In conclusion, the produced hydrogel composite scaffold holds great promise for meniscus tissue engineering.Article Citation - WoS: 9Citation - Scopus: 9Development of an Improved Amplex Red Peroxidation Activity Assay for Screening Cytochrome P450 Variants and Identification of a Novel Mutant of the Thermophilic Cyp119(Springer, 2020) Başlar, M. Semih; Sakallı, Tuğçe; Güralp, Gülce; Kestevur Doğru, Ekin; Haklı, Emre; Sürmeli, Nur BaşakBiocatalysts are increasingly utilized in the synthesis of drugs and agrochemicals as an alternative to chemical catalysis. They are preferred in the synthesis of enantiopure products due to their high regioselectivity and enantioselectivity. Cytochrome P450 (P450) oxygenases are valuable biocatalysts, since they catalyze the oxidation of carbon-hydrogen bonds with high efficiency and selectivity. However, practical use of P450s is limited due to their need for expensive cofactors and electron transport partners. P450s can employ hydrogen peroxide (H2O2) as an oxygen and electron donor, but the reaction with H(2)O(2)is inefficient. The development of P450s that can use H(2)O(2)will expand their applications. Here, an assay that utilizes Amplex Red peroxidation, to rapidly screen H2O2-dependent activity of P450 mutants in cell lysate was developed. This assay was employed to identify mutants of CYP119, a thermophilic P450 fromSulfolobus acidocaldarius, with increased peroxidation activity. A mutant library of CYP119 containing substitutions in the heme active site was constructed via combinatorial active-site saturation test and screened for improved activity. Screening of 158 colonies led to five mutants with higher activity. Among improved variants, T213R/T214I was characterized. T213R/T214I exhibited fivefold higherk(cat)for Amplex Red peroxidation and twofold higherk(cat)for styrene epoxidation. T213R/T214I showed higher stability towards heme degradation by H2O2. While theK(m)for H(2)O(2)and styrene were not altered by the mutation, a fourfold decrease in the affinity for another substrate, lauric acid, was observed. In conclusion, Amplex Red peroxidation screening of CYP119 mutants yielded enzymes with increased peroxide-dependent activity. [GRAPHICS] .Article Citation - WoS: 14Citation - Scopus: 15Development and Verification of a Three-Dimensional (3d) Breast Cancer Tumor Model Composed of Circulating Tumor Cell (ctc) Subsets(Springer, 2020) Anıl İnevi, Müge; Sağlam Metiner, Pelin; Kabak, Evrim Ceren; Gülce İz, SultanBreast cancer is one of the most common cancer types among women in which early tumor invasion leads to metastases and death. EpCAM (epithelial cellular adhesion molecule) and HER2 (human epidermal growth factor receptor 2) are two main circulating tumor cell (CTC) subsets in HER2+ breast cancer patients. In this regard, the main aim of this study is to develop and characterize a three-dimensional (3D) breast cancer tumor model composed of CTC subsets to evaluate new therapeutic strategies and drugs. For this reason, EpCAM(+) and HER2(+) sub-populations were isolated from different cell lines to establish 3D tumor model that mimics in situ (in vivo) more closely than two-dimensional (2D) models. EpCAM(+)/HER2(+) cells had a high proliferation rate and low tendency to attach to the surface in comparison with parental MDA-MB-453 cells as CTC subsets. Aggressive breast cancer subpopulations cultured in 3D porous chitosan scaffold had enhanced cell-cell and cell-matrix interactions compared to 2D cultured cells and these 3D models showed more aggressive morphology and behavior, expressed higher levels of pluripotency marker genes, Nanog, Sox2 and Oct4. For the verification of the 3D model, the effects of doxorubicin which is a chemotherapeutic agent used in breast cancer treatment were examined and increased drug resistance was determined in 3D cultures. The 3D tumor model comprising EpCAM(+)/HER2(+) CTC subsets developed in this study has a promising potential to be used for investigation of an aggressive CTC microenvironment in vitro that mimics in vivo characteristics to test new drug candidates against CTCs.Article Citation - WoS: 3Citation - Scopus: 5A Novel Thermophilic Hemoprotein Scaffold for Rational Design of Biocatalysts(Springer Verlag, 2018) Efua Aggrey Fynn, Joana; Sürmeli, Nur BaşakHemoproteins are commonly found in nature, and involved in many important cellular processes such as oxygen transport, electron transfer, and catalysis. Rational design of hemoproteins can not only inspire novel biocatalysts but will also lead to a better understanding of structure-function relationships in native hemoproteins. Here, the heme nitric oxide/oxygen-binding protein from Caldanaerobacter subterraneus subsp. tengcongensis (TtH-NOX) is used as a novel scaffold for oxidation biocatalyst design. We show that signaling protein TtH-NOX can be reengineered to catalyze H2O2 decomposition and oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) by H2O2. In addition, the role of the distal tyrosine (Tyr140) in catalysis is investigated. The mutation of Tyr140 to alanine hinders the catalysis of the oxidation reactions. On the other hand, the mutation of Tyr140 to histidine, which is commonly observed in peroxidases, leads to a significant increase of the catalytic activity. Taken together, these results show that, while the distal histidine plays an important role in hemoprotein reactions with H2O2, it is not always essential for oxidation activity. We show that TtH-NOX protein can be used as an alternative scaffold for the design of novel biocatalysts with desired reactivity or functionality. H-NOX proteins are homologous to the nitric oxide sensor soluble guanylate cyclase. Here, we show that the gas sensor protein TtH-NOX shows limited capacity for catalysis of redox reactions and it can be used as a novel scaffold in biocatalysis design. [GRAPHICS] .Article Citation - WoS: 17Citation - Scopus: 22Adhesive Bonding Strategies To Fabricate High-Strength and Transparent 3d Printed Microfluidic Device(American Institute of Physics, 2020) Keçili, Seren; Tekin, Hüseyin CumhurRecently, the use of 3D printing technologies has become prevalent in microfluidic applications. Although these technologies enable low-cost, rapid, and easy fabrication of microfluidic devices, fabricated devices suffer from optical opaqueness that inhibits their use for microscopic imaging. This study investigates bonding strategies using polydimethylsiloxane (PDMS) and printer resin as interlayer materials to fabricate high-strength optically transparent 3D-printed microfluidic devices. First, we fabricated microfluidic structures using a stereolithography 3D printer. We placed 3D-printed structures on interlayer materials coated surfaces. Then, we either let these 3D-printed structures rest on the coated slides or transferred them to new glass slides. We achieved bonding between 3D-printed structures and glass substrates with UV exposure for resin and with elevated temperature for PDMS interlayer materials. Bonding strength was investigated for different interlayer material thicknesses. We also analyzed the bright-field and fluorescence imaging capability of microfluidic devices fabricated using different bonding strategies. We achieve up to twofold (9.1 bar) improved bonding strength and comparable fluorescence sensitivity with respect to microfluidic devices fabricated using the traditional plasma activated PDMS-glass bonding method. Although stereolithography 3D printer allows fabrication of enclosed channels having dimensions down to similar to 600 mu m, monolithic transparent microfluidic channels with 280 x 110 mu m(2) cross section can be realized using adhesive interlayers. Furthermore, 3D-printed microfluidic chips can be integrated successfully with Protein-G modified substrates using resin interlayers for detection of fluorescent-labeled immunoglobulin down to similar to 30 ng/ml. Hence, this strategy can be applied to fabricate high-strength and transparent microfluidic chips for various optical imaging applications including biosensing.Article Citation - WoS: 13Citation - Scopus: 13Cycloartane-Type Sapogenol Derivatives Inhibit Nf?b Activation as Chemopreventive Strategy for Inflammation-Induced Prostate Carcinogenesis(Elsevier Ltd., 2018) Debeleç Bütüner, Bilge; Öztürk, Mert Burak; Tağ, Özgür; Akgün, İsmail Hakkı; Yetik Anacak, Günay; Bedir, Erdal; Korkmaz, Kemal SamiChronic inflammation is associated to 25% of cancer cases according to epidemiological data. Therefore, inhibition of inflammation-induced carcinogenesis can be an efficient therapeutic approach for cancer chemoprevention in drug development studies. It is also determined that anti-inflammatory drugs reduce cancer incidence. Cell culture-based in vitro screening methods are used as a fast and efficient method to investigate the biological activities of the biomolecules. In addition, saponins are molecules that are isolated from natural sources and are known to have potential for tumor inhibition. Studies on the preparation of analogues of cycloartane-type sapogenols (9,19-cyclolanostanes) have so far been limited. Therefore we have decided to direct our efforts toward the exploration of new anti-tumor agents prepared from cycloastragenol and its production artifact astragenol. The semi-synthetic derivatives were prepared mainly by oxidation, condensation, alkylation, acylation, and elimination reactions. After preliminary studies, five sapogenol analogues, two of which were new compounds (2 and 3), were selected and screened for their inhibitory activity on cell viability and NFκB signaling pathway activity in LNCaP prostate cancer cells. We found that the astragenol derivatives 1 and 2 as well as cycloastragenol derivatives 3, 4, and 5 exhibited strong inhibitory activity on NFκB signaling leading the repression of NFκB transcriptional activation and suppressed cell proliferation. The results suggested that these molecules might have significant potential for chemoprevention of prostate carcinogenesis induced by inflammatory NFκB signaling pathway.Article Citation - WoS: 11Citation - Scopus: 11Secondary Metabolites From Astragalus Karjaginii Boriss and the Evaluation of Their Effects on Cytokine Release and Hemolysis(Elsevier Ltd., 2017) Aslanipour, Behnaz; Gülcemal, Derya; Nalbantsoy, Ayşe; Yusufoğlu, Hasan; Bedir, ErdalA new cycloartane sapogenol and a new cycloartane xyloside were isolated from Astragalus karjaginii BORISS along with thirteen known compounds. The structures of the new compounds were established as 3-oxo-6α,16β,24(S),25-tetrahydroxycycloartane (1) and 6-O-β-D-xylopyranosyl-3β,6α,16β,24(S),25-pentahydroxycycloartane (2) by 1D- and 2D-NMR experiments as well as ESIMS and HRMS analyses. The presence of the keto function at position 3 was reported for the first time for cyclocanthogenol sapogenin of Astragalus genus. In vitro immunomodulatory effects of the new compounds (1 and 2) along with the n-BuOH and MeOH extracts of A. karjaginii at two different doses (3 and 6 μg) were tested on human whole blood for in vitro cytokine release (IL-2, IL-17A and IFN-γ) and hemolytic activities. The results confirmed that compound 2, a monodesmosidic saponin, had the strongest effect on the induction of both IL-2 (6 μg, 6345.41 ± 0.12 pg/mL (× 5), P < 0.001) and a slight effect upon IL-17A (3 μg, 5217.85 ± 0.72 pg/mL, P < 0.05) cytokines compared to the other test compounds and positive controls (AST VII: Astragaloside VII; and QS-21: Quillaja saponin 21). All tested extracts and molecules also induced release of IFN-γ remarkably ranging between 5031.95 ± 0.05 pg/mL, P < 0.001 for MeOH extract (6 μg) and 5877.08 ± 0.06 pg/mL, P < 0.001 for compound 1 (6 μg) compared to QS-21 (6 μg, 5924.87 ± 0.1 pg/mL, P < 0.001). Administration of AST VII and other test compounds did not cause any hemolytic activity, whereas QS-21 resulted a noteworthy hemolysis.