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: 4Citation - Scopus: 3An Investigation of Rna Methylations With Biophysical Approaches in a Cervical Cancer Cell Model(Mdpi, 2024) Saglam, Buket; Akkus, Onur; Akcaoz-Alasar, Azime; Ceylan, Cagatay; Guler, Gunnur; Akgul, BunyaminRNA methylation adds a second layer of genetic information that dictates the post-transcriptional fate of RNAs. Although various methods exist that enable the analysis of RNA methylation in a site-specific or transcriptome-wide manner, whether biophysical approaches can be employed to such analyses is unexplored. In this study, Fourier-transform infrared (FT-IR) and circular dichroism (CD) spectroscopy are employed to examine the methylation status of both synthetic and cellular RNAs. The results show that FT-IR spectroscopy is perfectly capable of quantitatively distinguishing synthetic m(6)A-methylated RNAs from un-methylated ones. Subsequently, FT-IR spectroscopy is successfully employed to assess the changes in the extent of total RNA methylation upon the knockdown of the m(6)A writer, METTL3, in HeLa cells. In addition, the same approach is shown to accurately detect reduction in total RNA methylation upon the treatment of HeLa cells with tumor necrosis factor alpha (TNF-alpha). It is also demonstrated that m(1)A and m(6)A methylation induce quite a distinct secondary structure on RNAs, as evident from CD spectra. These results strongly suggest that both FT-IR and CD spectroscopy methods can be exploited to uncover biophysical properties impinged on RNAs by methyl moieties, providing a fast, convenient and cheap alternative to the existing methods.Article Citation - WoS: 2Citation - Scopus: 1A Safe Fiber-Optic-Sensor-Assisted Industrial Microwave-Heating System(Mdpi, 2024) Yuksel, Kivilcim; Merdin, Oguz Deniz; Kinet, Damien; Merdin, Murat; Guyot, Corentin; Caucheteur, ChristopheIndustrial microwave-heating systems are pivotal in various sectors, including food processing and materials manufacturing, where precise temperature control and safety are critical. Conventional systems often struggle with uneven heat distribution and high fire risks due to the intrinsic properties of microwave heating. In this work, a fiber-optic-sensor-assisted monitoring system is presented to tackle the pressing challenges associated with uneven heating and fire hazards in industrial microwave systems. The core innovation lies in the development of a sophisticated fiber-optic 2D temperature distribution sensor and a dedicated fire detector, both designed to significantly mitigate risks and optimize the heating process. Experimental results set the stage for future innovations that could transform the landscape of industrial heating technologies toward better process quality.Review Citation - WoS: 1Citation - Scopus: 2Bergamot (<i>citrus Bergamia</I>), a (poly)phenol-Rich Source for Improving Osteosarcopenic Obesity: a Systematic Review(Mdpi, 2024) Mazzola, Giuseppe; Rondanelli, Mariangela; Baron, Giovanna; Zupo, Roberta; Castellana, Fabio; Clodoveo, Maria Lisa; Perna, SimoneThis systematic review investigates the potential of bergamot, a polyphenol-rich citrus fruit, in improving osteosarcopenic obesity, a condition characterized by the simultaneous presence of osteoporosis, obesity, and sarcopenia. Bergamot extracts have been suggested to possess several pharmacological properties, including anti-inflammatory and antioxidant effects, which could be useful in the management of age-related diseases and neuromuscular health. The review highlights the promising effects of bergamot extracts on skeletal muscle mass and function, particularly in the context of obesity, metabolic syndrome, osteosarcopenic obesity, and osteoporosis. Furthermore, some studies have shown that bergamot extracts can improve the metabolic balance, endothelial function, and maximal oxygen uptake in athletes, highlighting their potential benefits for skeletal muscle health. Taken together, these results suggest that bergamot extracts, especially those rich in polyphenols, may be a valuable adjunct in the management of osteosarcopenic obesity and other associated clinical conditions involving pro-inflammatory effects on organs and tissues.Review Citation - WoS: 10Citation - Scopus: 12Genetic and Biotechnological Approaches To Improve Fruit Bioactive Content: a Focus on Eggplant and Tomato Anthocyanins(Mdpi, 2024) Cammareri, Maria; Frary, Amy; Frary, Anne; Grandillo, SilvanaAnthocyanins are a large group of water-soluble flavonoid pigments. These specialized metabolites are ubiquitous in the plant kingdom and play an essential role not only in plant reproduction and dispersal but also in responses to biotic and abiotic stresses. Anthocyanins are recognized as important health-promoting and chronic-disease-preventing components in the human diet. Therefore, interest in developing food crops with improved levels and compositions of these important nutraceuticals is growing. This review focuses on work conducted to elucidate the genetic control of the anthocyanin pathway and modulate anthocyanin content in eggplant (Solanum melongena L.) and tomato (Solanum lycopersicum L.), two solanaceous fruit vegetables of worldwide relevance. While anthocyanin levels in eggplant fruit have always been an important quality trait, anthocyanin-based, purple-fruited tomato cultivars are currently a novelty. As detailed in this review, this difference in the anthocyanin content of the cultivated germplasm has largely influenced genetic studies as well as breeding and transgenic approaches to improve the anthocyanin content/profile of these two important solanaceous crops. The information provided should be of help to researchers and breeders in devising strategies to address the increasing consumer demand for nutraceutical foods.Article Citation - WoS: 5Citation - Scopus: 5Mechanical Behaviour of Photopolymer Cell-Size Graded Triply Periodic Minimal Surface Structures at Different Deformation Rates(Mdpi, 2024) Yilmaz, Yunus Emre; Novak, Nejc; Al-Ketan, Oraib; Erten, Hacer Irem; Yaman, Ulas; Mauko, Anja; Ren, ZoranThis study investigates how varying cell size affects the mechanical behaviour of photopolymer Triply Periodic Minimal Surfaces (TPMS) under different deformation rates. Diamond, Gyroid, and Primitive TPMS structures with spatially graded cell sizes were tested. Quasi-static experiments measured boundary forces, representing material behaviour, inertia, and deformation mechanisms. Separate studies explored the base material's behaviour and its response to strain rate, revealing a strength increase with rising strain rate. Ten compression tests identified a critical strain rate of 0.7 s-1 for "Grey Pro" material, indicating a shift in failure susceptibility. X-ray tomography, camera recording, and image correlation techniques observed cell connectivity and non-uniform deformation in TPMS structures. Regions exceeding the critical rate fractured earlier. In Primitive structures, stiffness differences caused collapse after densification of smaller cells at lower rates. The study found increasing collapse initiation stress, plateau stress, densification strain, and specific energy absorption with higher deformation rates below the critical rate for all TPMS structures. However, cell-size graded Primitive structures showed a significant reduction in plateau and specific energy absorption at a 500 mm/min rate.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.Review Citation - WoS: 20Citation - Scopus: 21An Overview of Current Detection Methods for Rna Methylation(Mdpi, 2024) Saglam, Buket; Akgul, BunyaminEpitranscriptomic mechanisms, which constitute an important layer in post-transcriptional gene regulation, are involved in numerous cellular processes under health and disease such as stem cell development or cancer. Among various such mechanisms, RNA methylation is considered to have vital roles in eukaryotes primarily due to its dynamic and reversible nature. There are numerous RNA methylations that include, but are not limited to, 2'-O-dimethyladenosine (m6Am), N7-methylguanosine (m7G), N6-methyladenosine (m6A) and N1-methyladenosine (m1A). These biochemical modifications modulate the fate of RNA by affecting the processes such as translation, target site determination, RNA processing, polyadenylation, splicing, structure, editing and stability. Thus, it is highly important to quantitatively measure the changes in RNA methylation marks to gain insight into cellular processes under health and disease. Although there are complicating challenges in identifying certain methylation marks genome wide, various methods have been developed recently to facilitate the quantitative measurement of methylated RNAs. To this end, the detection methods for RNA methylation can be classified in five categories such as antibody-based, digestion-based, ligation-based, hybridization-based or direct RNA-based methods. In this review, we have aimed to summarize our current understanding of the detection methods for RNA methylation, highlighting their advantages and disadvantages, along with the current challenges in the field.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.