TR-Dizin İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/396
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Article Bazı geleneksel Türk gıdalarından laktik asit bakterilerinin izolasyonu(2021) DOĞAN Osman; CEBECİ AysunAmaç: Bu çalışma ülkemizde geleneksel yöntemlerle üretilen gıda ürünlerindenlaktik asit bakterilerinin izolasyonunu ve tanımlanmasını sağlamak amacıylayapılmıştır.Materyal ve Yöntem: Çalışma kapsamında Van otlu peynir ve ekşi hamur örneğikullanılmıştır. Bu örnekler içerdikleri laktik asit bakterileri için çalışılmış vetanımlanmaları için biyokimyasal ve PCR bazlı moleküler biyolojik tekniklere tabitutulmuşlardır. Biyokimyasal testler kapsamında örnekler, Gram reaksiyonları,katalaz aktivitesi, gaz üretimi, 10oC ve 45oC'de, %6 ve %16 NaCl konsantrasyonda,pH 4.4 ve pH 9.6’da gelişim göstermeleri açısından incelenmiştir. Moleküler biyolojideneyleri kapsamında ise tür ve suş düzeyinde tanımlama için PCR-RFLP, 16SrRNA gen dizileme ve RAPD-PCR teknikleri kullanılmıştır.Araştırma Bulguları: Bir dizi mikrobiyolojik deneylerin sonucunda 26 adet bakteripotansiyel laktik asit bakterisi olarak izole edilmiştir. Bunlardan 25 adedininLactobacillus, Pediococcus ve Enterococcus cinslerine ait olduğu tespit edilmiş vetür ve suş düzeyinde tanımlanmaları sağlanmıştır. Kalan bir adet izolat iseStaphylococcus hominis olarak tanımlanmıştır.Sonuç: Çalışmamız sonucunda 25 adet laktik asit bakterisi gen dizileme ve RAPDPCR teknikleri kullanılarak tür ve suş düzeyinde başarıyla tanımlanmıştır.Article Citation - Scopus: 2Zeolite Synthesis by Alkali Fusion Method Using Two Different Fly Ashes Derived From Turkish Thermal Power Plants(Chamber of Mining Engineers of Turkey, 2020-03-01) Top, S.; Vapur, HüseyinIn this study, Faujasite (Na-LSX) (3.5(Ca0.3)3.5(Na0.6)3.5(Mg0.1)Al7Si17O48 32(H2O)) type zeolites and Ca-Filipsite (CaK0.6Na0.4Si5.2Al2.8O16 6(H2O)) type zeolites were produced from Sugözü Thermal Power Plant and Çatalaǧzi Thermal Power Plant fly ashes by alkali fusion method followed by water leaching, respectively. In these methods, fly ashes and sodium hydroxide (NaOH) were mixed in certain proportions and sintered at 600°C in ash furnace. Then, zeolites were obtained from the ground materials after water leaching and solid/liquid separation, respectively. Cation Exchange Capacity (CEC), X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM), Fourier-Transform Infrared Spectroscopy (FTIR), X-Ray Fluorescence (XRF) and Atomic Absorption Spectrometer (AAS) analyses were used to characterize the synthesized zeolites. The zeolites synthesized with Sugözü fly ashes in a ratio of 1:2 had 136.93 meq/100 g CEC, whereas the CEC of synthesized zeolite from Çatalaǧzi fly ashes was found to be 247.88 meq/100 g. As a result, zeolites, which can be used as wastewater treatment agent, energy storage material, catalyst and separator, were synthesized by using 2 different Class F fly ash. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 6Citation - Scopus: 6Sex Effect on the Correlation of Immunoglobulin G Glycosylation With Rheumatoid Arthritis Disease Activity(Tubitak Scientific & Technological Research Council Turkey, 2020-12-14) Ercan, AltanRheumatoid arthritis (RA) is a chronic autoimmune disease which affects females more than males with a presence of autoantibodies. Immunoglobulin G (IgG) produced by adaptive arm has 2 functional domains, Fc and Fab. The Fc domain binds Fc gamma receptors and C1q proteins of the innate arm. Therefore, the IgG Fc domain serves as a bridge between the innate and adaptive arms and is regulated by an evolutionarily conserved N-glycosylation with variable structures. These glycans are classified as agalactosylated G0, monogalactosylated G1, and digalactosylated G2, which are further modified by core-fucosylation (F) and bisecting N-acetylglucosamine (B) moieties such as G0F and G0FB. Interestingly, proinflammatory G0F is shown to be regulated by estrogen in vivo. Here, it is hypothesized that the regulation of G0F by estrogen contributes to sex dichotomy in RA by setting up the level of IgG-dependent inflammation and therefore, RA disease activity (Das28-CRP3). To investigate this hypothesis, IgG glycosylation was characterized in serum samples from active RA patients (n = 232) and healthy controls (n = 232) by serum N-glycan analysis using the high performance liquid chromatography. According to the results, the IgG Fc glycan phenotype originates predominantly from the structure of G0F, and both G0F and G0FB correlate with Das28-CRP3 in females, but not in males. In conclusion, IgG G0F-dependent inflammation differs in males and females, and these differences point to the differential regulation of inflammation by sex hormone estrogen via IgG glycosylation.Article Citation - WoS: 1Citation - Scopus: 1RPI-1 (Human DCDC2) Displays Functional Redundancy With Nephronophthisis 4 in Regulating Cilia Biogenesis in C. Elegans(Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Kaplan, Oktay I.Projecting from most cell surfaces, cilia serve as important hubs for sensory and signaling processes and have been linked to a variety of human disorders, including Bardet-Biedl Syndrome (BBS), Meckel-Gruber Syndrome (MKS), Nephronophthisis (NPHP), and Joubert Syndrome, and these diseases are collectively known as a ciliopathy. DCDC2 is a ciliopathy protein that localizes to cilia; nevertheless, our understanding of the role of DCDC2 in cilia is still limited. We employed C. elegans to investigate the function of C. elegans RPI-1, a Caenorhabditis elegans ortholog of human DCDC2, in cilia and found that C. elegans RPI-1 localizes to the entire ciliary axoneme, but is not present in the transition zone and basal body. We generated a null mutant of C. elegans rpi-1, and our analysis with a range of fluorescence-based ciliary markers revealed that DCDC2 and nephronophthisis 4 (NPHP-4/NPHP4) display functional redundant roles in regulating cilia length and cilia positions. Taken together, our analysis discovered a novel genetic interaction between two ciliopathy disease genes (RPI-1/DCDC2 and NPHP-4/NPHP4) in C. elegans.Article Citation - WoS: 3Citation - Scopus: 3MicroRNA Prediction Based on 3D Graphical Representation of RNA Secondary Structures(Tubitak Scientific & Technological Research Council Turkey, 2019-08-05) Sacar Demirci, Muserref Duygu; Demirci, Müşerref Duygu SaçarMicroRNAs (miRNAs) are posttranscriptional regulators of gene expression. While a miRNA can target hundreds of messenger RNA (mRNAs), an mRNA can be targeted by different miRNAs, not to mention that a single miRNA might have various binding sites in an mRNA sequence. Therefore, it is quite involved to investigate miRNAs experimentally. Thus, machine learning (ML) is frequently used to overcome such challenges. The key parts of a ML analysis largely depend on the quality of input data and the capacity of the features describing the data. Previously, more than 1000 features were suggested for miRNAs. Here, it is shown that using 36 features representing the RNA secondary structure and its dynamic 3D graphical representation provides up to 98% accuracy values. In this study, a new approach for ML-based miRNA prediction is proposed. Thousands of models are generated through classification of known human miRNAs and pseudohairpins with 3 classifiers: decision tree, naive Bayes, and random forest. Although the method is based on human data, the best model was able to correctly assign 96% of nonhuman hairpins from MirGeneDB, suggesting that this approach might be useful for the analysis of miRNAs from other species.Article Citation - Scopus: 2Impact of High Speed Railway Systems on Inter-Regional Trips and Accessibility in Turkey(Istanbul Teknik Universitesi, Faculty of Architecture itudergisi@itu.edu.tr, 2020) Baş, Ahmet; Yüzer, Mehmet AliHigh-speed trains are faster, safer, more comfortable than road transport for trips of 250–1000 kilometers. Accordingly, a significant increase has been observed in inter-city railway transport following the construction of high-speed railway (HSR) connections. The present study shows the effects of HSR on accessibility and potential savings in time when compared to other transportation modes. The time saved by HSR systems has been shown to change purpose trip. The level of accessibility provided by the HSR between Konya–Ankara–Istanbul link is compared with the accessibility of other travel modes through an investigation of the weighted average travel times and an analysis of costs. Furthermore, data gathered from a field study carried out among users of the Konya-Ankara HSR link is used to identify the distribution of travel choices among different transportation modes, based on such social and economic indicators as income, car ownership and employment status. It is found that HSR service increases accessibility between cities, and changes travel demands and purpose, in favor of railways, and that economic factors such as income and car ownership are important in the use of HSR services. Finally, this research identifies social and cultural activities as a new reason for travel, in which users diversify their travel destinations because of the time savings offered by HSR systems. © 2020 Elsevier B.V., All rights reserved.Article Citation - Scopus: 2Evaluating the Microbial Growth Kinetics and Artificial Gastric Digestion Survival of a Novel Pichia Kudriavzevii FOL-04(Field Crops Central Research Institute, 2022-06-15) Gumustop, Ismail; Ortakci, FatihPresent study aims to explore Pichia kudriavzevii FOL-04 (FOL-04)’s: i) survival against artificial gastric juice (AGJ) and artificial bile juice (ABJ), ii) growth kinetics in shake flask (SF) and fed-batch trials (FBT). Survival of FOL-04 as measured by relative cell density (RCD) against AGJ and ABJ was screened at four different pH-levels (control, 3, 2, 1.5) and ox-bile concentrations (control, 0.2%, 1%, 2%), respectively. Growth kinetics was calculated by periodic measurement of OD<inf>600</inf> in SF (225 rpm, 30°C) or in FBT using exponential feeding regimen where pH, dissolved-oxygen and temperature were controlled at 5.5, 21%, and 30°C, respectively. The doubling-time, maximum specific growth rate, and final cell densities achieved for SF and FBT were 81.7min, 1.67, 11.79 and 170.4 min, 4.75, 37.95, respectively. RCDs calculated were similar for pH=3 and control vs both were significantly higher(p<0.05) than pH=1.5 and 2 with the latter two pH-levels were not significantly different(p>0.05). RCDs were similar across control, 0.2%, and 1% ox-bile levels(p>0.05). However, 2% ox-bile yielded significantly lower RCD (p<0.05) compared to all except 1%. FOL-04 is a potential probiotic candidate showing robustness against AGJ and ABJ and remarkable biomass increase was achieved when grown under FBT which could pave the way for developing a yeast-based probiotic using this strain. © 2023 Elsevier B.V., All rights reserved.Article Enlightening the Molecular Mechanisms of Type 2 Diabetes With a Novel Pathway Clustering and Pathway Subnetwork Approach(Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Bakir-Gungor, Burcu; Yazici, Miray Unlu; Goy, Gokhan; Temiz, Mustafa; Ünlü Yazici, MirayType 2 diabetes mellitus (T2D) constitutes 90% of the diabetes cases, and it is a complex multifactorial disease. In the last decade, genome-wide association studies (GWASs) for T2D successfully pinpointed the genetic variants (typically single nucleotide polymorphisms, SNPs) that associate with disease risk. In order to diminish the burden of multiple testing in GWAS, researchers attempted to evaluate the collective effects of interesting variants. In this regard, pathway-based analyses of GWAS became popular to discover novel multigenic functional associations. Still, to reveal the unaccounted 85 to 90% of T2D variation, which lies hidden in GWAS datasets, new post-GWAS strategies need to be developed. In this respect, here we reanalyze three metaanalysis data of GWAS in T2D, using the methodology that we have developed to identify disease-associated pathways by combining nominally significant evidence of genetic association with the known biochemical pathways, protein-protein interaction (PPI) networks, and the functional information of selected SNPs. In this research effort, to enlighten the molecular mechanisms underlying T2D development and progress, we integrated different in silico approaches that proceed in top-down manner and bottom-up manner, and presented a comprehensive analysis at protein subnetwork, pathway, and pathway subnetwork levels. Using the mutual information based on the shared genes, the identified protein subnetworks and the affected pathways of each dataset were compared. While most of the identified pathways recapitulate the pathophysiology of T2D, our results show that incorporating SNP functional properties, PPI networks into GWAS can dissect leading molecular pathways, and it could offer improvement over traditional enrichment strategies.Article Citation - Scopus: 1Electricity Load Forecasting Using Deep Learning and Novel Hybrid Models(Sakarya University, 2022-02-28) Sutcu, Muhammed; Şahi̇n, Kübra Nur; Koloğlu, Yunus; Çelikel, Mevlüt Emirhan; Gulbahar, Ibrahim TümayLoad forecasting is an essential task which is executed by electricity retail companies. By predicting the demand accurately, companies can prevent waste of resources and blackouts. Load forecasting directly affect the financial of the company and the stability of the Turkish Electricity Market. This study is conducted with an electricity retail company, and main focus of the study is to build accurate models for load. Datasets with novel features are preprocessed, then deep learning models are built in order to achieve high accuracy for these problems. Furthermore, a novel method for solving regression problems with classification approach (discretization) is developed for this study. In order to obtain more robust model, an ensemble model is developed and the success of individual models are evaluated in comparison to each other. © 2025 Elsevier B.V., All rights reserved.Article Effects of Dry Particle Coating With Nano-and Microparticles on Early Compressive Strength of Portland Cement Pastes(Tulpar Academic Publishing, 2021-12-16) Yorulmaz, Hediye; Özuzun, Sümeyye; Uzal, Burak; İLkentapar, Serhan; Durak, Uğur; Karahan, Okan; Atis, C. D.It is known that nano-and microparticles have been very popular in recent years since their advantages. However, due to the very small size of such materials, they have very high tendency to agglomeration particularly for nanoparticles. Therefore, it is critical that they are properly distributed in the system to which they are added. This paper investigated the effects of dry particle coating with nano-and microparticles to solve the agglomeration problem. For a clear evaluation, paste samples were preferred to detemine the compressive strength. Nano-SiO<inf>2</inf> and nano-CaCO<inf>3</inf>, microCaCO<inf>3</inf> and micro-SiO<inf>2</inf>, also known as silica fume, were selected as particulate additives. It was studied by the addition of various percentages (0.3, 0.7, 1, 2, 3 and 5%) of nano-and microparticles in cementitious systems, replacing cement by weight with and without dry particle coating. Dry particle coating was made by using a highspeed paddle mixer. Portland cement and additive particles were mixed at 1500 rpm for 30 seconds in high-speed powder mixer designed for this purpose. The 3-day compressive strength of the cement-based samples to which particles were added at the specified rates was determined and the effect of the dry particle coating on the early strength was investigated. According to the results, it was observed that the production of paste with the dry particle coating technique gave higher compressive strength compared to the production of paste directly in early period. Especially with dry particle coating, compressive strength increased more than 100% in paste samples containing 0.3% nano-SiO<inf>2</inf> compared to direct addition without coating. © 2024 Elsevier B.V., All rights reserved.
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