PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 1Citation - Scopus: 1Improved Isolation of Ultra-High Genomic Dna Suitable for Third-Generation Sequencing(Mdpi, 2025) Ova, Ayse Oyku; Joffre, Enrique; Shafagh, Reza Zandi; Assuncao, Mariana F. G.; Sidorov, Roman Y.; Santos, Lilia M. A.; Romling, UteAlthough a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing. The designed experimental approach is simple, but effective in isolating high-quality ultra-long genomic DNA that is suitable for third-generation sequencing by Oxford Nanopore Technology from challenging bacterial samples. We envisage that genomic DNA isolation using the incubation chamber, or variations thereof, will facilitate the regular sequencing of megabasepair-long DNA fragments, with a multitude of applications in microbiology, immunology, oncology, paleontology and forensic science.Article Citation - WoS: 6Citation - Scopus: 6Comparison of Linear and Nonlinear Twist Extrusion Processes With Crystal Plasticity Finite Element Analysis(Mdpi, 2024) Simsek, Ulke; Davut, Kemal; Miyamoto, Hiroyuki; Yalcinkaya, TuncayThe mechanical characteristics of polycrystalline metallic materials are influenced significantly by various microstructural parameters, one of which is the grain size. Specifically, the strength and the toughness of polycrystalline metals exhibit enhancement as the grain size is reduced. Applying severe plastic deformations (SPDs) has a noticeable result in obtaining metallic materials with ultrafine-grained (UFG) microstructure. SPD, executed through conventional shaping methods like extrusion, plays a pivotal role in the evolution of the texture, which is closely related to the plastic behavior and ductility. A number of SPD processes have been developed to generate ultrafine-grained materials, each having a different shear deformation mechanism. Among these methods, linear twist extrusion (LTE) presents a non-uniform and non-monotonic form of severe plastic deformation, leading to significant shifts in the microstructure. Prior research demonstrates the capability of the LTE process to yield consistent, weak textures in pre-textured copper. However, limitations in production efficiency and the uneven distribution of grain refinement have curbed the widespread use of LTE in industrial settings. This has facilitated the development of an improved novel method, that surpasses the traditional approach, known as the nonlinear twist extrusion procedure (NLTE). The NLTE method innovatively adjusts the channel design of the mold within the twist section to mitigate strain reversal and the rotational movement of the workpiece, both of which have been identified as shortcomings of twist extrusion. Accurate anticipation of texture changes in SPD processes is essential for mold design and process parameter optimization. The performance of the proposed extrusion technique should still be studied. In this context, here, a single crystal (SC) of copper in billet form, passing through both LTE and NLTE, is analyzed, employing a rate-dependent crystal plasticity finite element (CPFE) framework. CPFE simulations were performed for both LTE and NLTE of SC copper specimens having <100> or <111> directions parallel to the extrusion direction initially. The texture evolution as well as the cross-sectional distribution of the stress and strain is studied in detail, and the performance of both processes is compared.Article Citation - WoS: 3Citation - Scopus: 3Comprehensive Analysis of Lutein and Loroxanthin in <i>scenedesmus Obliquus</I>: From Quantification To Isolation(Mdpi, 2024) Erdogan, Aysegul; Karatas, Ayca Busra; Demir, Dilan; Demirel, Zeliha; Akturk, Merve; Copur, Oyku; Conk-Dalay, MeltemCarotenoids are hydrophobic pigments produced exclusively by plants, fungi, and specific microbes. Microalgae are well suited for the production of valuable carotenoids due to their rapid growth, efficient isoprenoid production pathway, and ability to store these compounds within their cells. The possible markets for bio-products range from feed additives in aquaculture and agriculture to pharmaceutical uses. The production of carotenoids in microalgae is affected by several environmental conditions, which can be utilized to enhance productivity. The current study focused on optimizing the extraction parameters (time, temperature, and extraction number) to maximize the yield of carotenoids. Additionally, the impact of various nitrogen sources (ammonia, nitrate, nitrite, and urea) on the production of lutein and loroxanthin in Scenedesmus obliquus was examined. To isolate the carotenoids, 0.20 g of biomass was added to 0.20 g of CaCO3 and 10.0 mL of ethanol solution containing 0.01% (w/v) pyrogallol. Subsequently, the extraction was performed using an ultrasonic bath for a duration of 10 min at a temperature of 30 degrees C. This was followed by a four-hour saponification process using a 10% methanolic KOH solution. The concentration of lutein and loroxanthin was measured using HPLC-DAD at 446 nm, with a flow rate of 1.0 mL/min using a Waters YMC C30 Carotenoid column (4.6 x 250 mm, 5 mu m). The confirmation of carotenoids after their isolation using preparative chromatography was achieved using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with an atmospheric pressure chemical ionization (APCI) probe and UV-vis spectroscopy. In summary, S. obliquus shows significant promise for the large-scale extraction of lutein and loroxanthin. The findings of this study provide strong support for the application of this technology to other species.