PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Integrative Bioinformatics Prediction of West Nile Virus-Derived microRNAs Reveals Potential Host Regulatory Interactions(Elsevier Sci Ltd, 2026-08) Demirci, Muserref Duygu Sacar; Orhan, Mehmet Emin; Erginkoc, Altay Nida; Saçar Demirci, Müşerref DuyguWest Nile virus (WNV) is a mosquito-borne flavivirus linked to severe neuroinvasive disease. Although host and vector microRNAs (miRNAs) have been implicated in viral infection, the presence and functional relevance of WNV-encoded miRNAs remain largely unexplored. Here, we developed an integrative bioinformatics pipeline that combines multiple miRNA prediction algorithms with secondary structure screening and host transcriptomic data to identify high-confidence candidate WNV-derived mature miRNAs. Overlap-based confidence scoring and differential expression support from RNA-seq datasets prioritized a small subset of putative miRNA-mRNA interactions with potential roles in infection-associated gene regulation. A competitive endogenous RNA network constructed from predicted mRNA, lncRNA, and circRNA targets highlighted pathways involving innate immunity, GPCR and Wnt signaling, RNA degradation, and viral replication. Together, these findings provide a reproducible computational workflow and nominate testable regulatory interactions for future experimental validation.Article Citation - WoS: 23Citation - Scopus: 28Ultra-Rapid Catalytic Degradation of 4-Nitrophenol With Ionic Liquid Recoverable and Reusable Ibuprofen Derived Silver Nanoparticles(Elsevier Sci Ltd, 2018-06) Hassan, Syeda Sara; Carlson, Krista; Mohanty, Swomitra Kumar; Sirajuddin; Canlier, AliThis study reports a one-pot and eco-friendly method for the synthesis of spherical ibuprofen derived silver nanoparticles (IBU-AgNPs) in aqueous media using ibuprofen analgesics drug as capping as well as reducing agent. Formation of AgNPs occurred within a few min (less than 5 min) at room temperature without resorting to any harsh conditions and hazardous organic solvents. Synthesized AgNPs were characterized with common analytical techniques. Transmission electron microscope (TEM) images confirmed the formation of spherical particles having a size distribution in the range of 12.5 +/- 1.5 nm. Employment of IBU analgesic aided the control of better size distribution and prevented agglomeration of particles. Such AgNPs solution was highly stable for more than two months when stored at ambient temperature. The IBU-AgNPs solution showed excellent ultra-rapid catalytic activity for the complete degradation of toxic 4-nitrophenol (4-NPh) into non-toxic 4-aminophenol (4-APh) within 40 s. AgNPs were recovered with the help of water insoluble-room temperature ionic liquid and reused with enhanced catalytic potential. This method provides a novel, rapid and economical alternative for the treatment of toxic organic pollutants to maintain water quality and environmental safety against water pollution. It is extendable for the control of other reducible contaminants in water as well. Furthermore, this catalytic activity for an effective degradation of organic toxins is expected to play a crucial role for achieving the Sustainable Development Goal 6 set by United Nations. (C) 2017 Elsevier Ltd. All rights reserved.Article Citation - WoS: 19Citation - Scopus: 23The Effects of Aerobic/Anoxic Period Sequence on Aerobic Granulation and COD/N Treatment Efficiency(Elsevier Sci Ltd, 2013-11) Ersan, Yusuf Cagatay; Erguder, Tuba HandeThe effects of period sequence (anoxic-aerobic and aerobic-anoxic) on aerobic granulation from suspended seed sludge, and COD, N removal efficiencies were investigated in two sequencing batch reactors. More stable granules with greater sizes (1.8-3.5 mm) were developed in R1 (anoxic-aerobic sequence). Yet, no significant difference was observed between the reactors in terms of removal efficiencies. Under optimum operational conditions, 92-95% COD, 89-90% TAN and 38-46% total nitrogen removal efficiencies were achieved. The anoxic-aerobic period sequence (R1) resulted in almost complete denitrification during anoxic periods while aerobic-anoxic sequence (R2) led to nitrate accumulation due to limited-carbon source and further granule disintegration. NH3-N concentration of 15-28 mg/L was found to inhibit COD removal up to 30%. This study also revealed the inhibitory sulfide production during anoxic periods. Sulfate concentration of 52.6-70.2 mg/L was found to promote sulfate reduction and sulfide generation (0.24-0.62 mg/L) which, together with free-ammonia, inhibited TAN oxidation by 10-50%. (C) 2013 Elsevier Ltd. All rights reserved.Article Citation - WoS: 118Citation - Scopus: 140Resistant Starch Type V Formation in Brown Lentil (Lens Culinaris Medikus) Starch With Different Lipids/Fatty Acids(Elsevier Sci Ltd, 2018-02) Okumus, Bahar Nur; Tacer-Caba, Zeynep; Kahraman, Kevser; Nilufer-Erdil, DilaraThis study aimed to characterize the brown lentil (Lens culinaris Medikus) starch and investigate the formation of amylose-lipid complexes (Resistant Starch Type V) by the addition of different lipids/fatty acids (10%, w/w) to both raw and cooked starch samples. Resistant starch content (measured by the official method of AACCI (Method 32-40), using the resistant starch assay kit) of raw brown lentil starch (BLS) increased significantly by the additions of lipids/fatty acids, starch sample complexed with HSO (hydrogenated sunflower oil) (14.1 +/- 0.4%) being the highest. For the cooked starch/lipid complexes, more profound effect was evident (22.2-67.7%). Peak, breakdown and trough viscosity values of the amylose-lipid complexed starches were significantly lower than that of BLS (p < 0.05), while significant decreases in the setback and final viscosities were only detected in oil samples, but not in fatty acids. Each lipid in concern exerted different effects on the digestibility of starch and amylose-lipid complex formation while having no substantial differential effects on the thermal properties of starch depicted by differential scanning calorimetry (DSC). Amylose-lipid complex formation with suitable fatty acids/lipids seems a promising way of increasing resistant starch content of food formulations. Although the applications being quite uncommon yet, brown lentil seems to have potential both as a starch and also as a resistant starch source.Article Citation - WoS: 7Citation - Scopus: 11Protein Β-Sheet Prediction Using an Efficient Dynamic Programming Algorithm(Elsevier Sci Ltd, 2017-10) Sabzekar, Mostafa; Naghibzadeh, Mahmoud; Eghdami, Mandie; Aydin, ZaferPredicting the beta-sheet structure of a protein is one of the most important intermediate steps towards the identification of its tertiary structure. However, it is regarded as the primary bottleneck due to the presence of non-local interactions between several discontinuous regions in beta-sheets. To achieve reliable long-range interactions, a promising approach is to enumerate and rank all beta-sheet conformations for a given protein and find the one with the highest score. The problem with this solution is that the search space of the problem grows exponentially with respect to the number of beta-strands. Additionally, brute force calculation in this conformational space leads to dealing with a combinatorial explosion problem with intractable computational complexity. The main contribution of this paper is to generate and search the space of the problem efficiently to reduce the time complexity of the problem. To achieve this, two tree structures, called sheet-tree and grouping-tree, are proposed. They model the search space by breaking it into sub-problems. Then, an advanced dynamic programming is proposed that stores the intermediate results, avoids repetitive calculation by repeatedly uses them efficiently in successive steps and reduces the space of the problem by removing those intermediate results that will no longer be required in later steps. As a consequence, the following contributions have been made. Firstly, more accurate beta-sheet structures are found by searching all possible conformations, and secondly, the time complexity of the problem is reduced by searching the space of the problem efficiently which makes the proposed method applicable to predict beta-sheet structures with high number of beta-strands. Experimental results on the BetaSheet916 dataset showed significant improvements of the proposed method in both execution time and the prediction accuracy in comparison with the state-of-the-art beta-sheet structure prediction methods Moreover, we investigate the effect of different contact map predictors on the performance of the proposed method using BetaSheet1452 dataset. The source code is available at http://www.conceptsgate.com/BetaTop.rar. (C) 2017 Elsevier Ltd. All rights reserved.Article Citation - WoS: 29Citation - Scopus: 41Optimisation of the Reaction Conditions for the Production of Cross-Linked Starch With High Resistant Starch Content(Elsevier Sci Ltd, 2015-05) Kahraman, Kevser; Koksel, Hamit; Ng, Perry K. W.The optimum reaction conditions (temperature and pH) for the preparation of cross-linked (CL) corn and wheat starches with maximum resistant starch (RS) content were investigated by using response surface methodology (RSM). According to the preliminary results, five levels were selected for reaction temperature (38-70 degrees C) and pH (10-12) in the main study. RS contents of the CL corn and wheat starch samples increased with increasing temperature and pH, and pH had a greater influence on RS content than had temperature. The maximum RS content (with a maximum p value of 0.4%) was obtained in wheat starch cross-linked at 38 degrees C and pH 12. In the case of CL corn starch, the optimum condition was 70 degrees C and pH 12. CL corn and wheat starch samples were also produced separately under the optimum conditions and their RS contents were 80.4% and 83.9%, respectively. These results were also in agreement with the values predicted by RSM. (C) 2014 Elsevier Ltd. All rights reserved.Article Citation - WoS: 36Citation - Scopus: 37Histopathological and Biomechanical Evaluation of Tenocyte Seeded Allografts on Rat Achilles Tendon Regeneration(Elsevier Sci Ltd, 2015-05) Gungormus, Cansin; Kolankaya, Durdane; Aydin, ErkinTendon injuries in humans as well as in animals' veterinary medicine are problematic because tendon has poor regenerative capacity and complete regeneration of the ruptured tendon is never achieved. In the last decade there has been an increasing need of treatment methods with different approaches. The aim of the current study was to improve the regeneration process of rat Achilles tendon with tenocyte seeded decellularized tendon matrices. For this purpose, Achilles tendons were harvested, decellularized and seeded as a mixture of three consecutive passages of tenocytes at a density of 1 x 10(6) cells/ml. Specifically, cells with different passage numbers were compared with respect to growth characteristics, cellular senescence and collagen/tenocyte marker production before seeding process. The viability of reseeded tendon constructs was followed postoperatively up to 6 months in rat Achilles tendon by histopathological and biomechanical analysis. Our results suggests that tenocyte seeded decellularized tendon matrix can significantly improve the histological and biomechanical properties of tendon repair tissue without causing adverse immune reactions. To the best of our knowledge, this is the first long-term study in the literature which was accomplished to prove the use of decellularized matrix in a clinically relevant model of rat Achilles tendon and the method suggested herein might have important implications for translation into the clinic. (C) 2015 Elsevier Ltd. All rights reserved.