Fen Edebiyat Fakültesi / Faculty of Letters and Sciences
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Publication 1-Methylhydantoin: From the Matrix Isolated Single Molecule to H-Bond Patterns Defining Different Polymorphs of the Compound(2017) Nogueira, Bernardo, A.; Canotilho, Joa; Eusebio, M. E. S.; Paixao, Antonia; Rui, Fausto; ILDIZ, GÜLCE ÖĞRÜÇ; 107326Publication 4-Hydroxyquinolin-2(1H)-One Isolated in Cryogenic Argon and Xenon Matrices: Tautomers and Photochemistry(Elsevier, 2024) Secrieru, A.; Lopes, S.; Nikitin, T.; Cristiano, Maria L. S.; FAUSTO, RUI4-Hydroxyquinolin-2(1H)-one (4HQ2O) was synthesized, isolated in cryogenic matrices (argon and xenon), and studied by infrared spectroscopy. Quantum chemical calculations carried out at the DFT(B3LYP)/6-311++G (3df,3pd) level of theory were used to determine the conformational and tautomeric properties of the molecule. Two tautomeric forms were identified in the as-deposited matrices with the help of the theoretical data. To investigate the photochemistry of the compound, in situ broadband ultraviolet (lambda > 283 nm) irradiation of the asdeposited argon matrix was performed. This irradiation led to the generation of an additional tautomer, together with the products of fragmentation of the heterocyclic ring of the molecule, specifically isocyanic acid and carbon monoxide. Photoproducts such as 1,3-dihydro-2H-indol-2-one and cyclohepta-1,2,4,6-tetraene were also observed in the photolyzed argon matrix. A comprehensive assignment of the infrared spectra of all the species observed experimentally is presented.Publication An Evaluation of Liminality in Nadine Gordimer's July's People(2020-03) KABAK, MURATSet during a civil war in the apartheid South Africa, Nadine Gordimer's July's People is centred around the relationship between the Smales family and their former servant July. As the communal ties disintegrate in the novel, three objects play a vital role in our understanding of the characters. For the purposes of this study, these symbols not only help us to reveal the nature of spatial-temporal dislocation but also reveal Gordimer's commentary on the apartheid South Africa. This study aims to contribute the existing scholarship by focusing on the liminal/in-between experience in July's People through analyzing the novel's preoccupation with subject-object relationship.Publication Analytic Functions With Conic Domains Associated With Certain Generalized q-integral Operator(Korean Mathematical Society, 2023) Ahuja, Om P.; ÇETİNKAYA, ASENA; Jain, Naveen KumarIn this paper, we define a new subclass of k-uniformly starlike functions of order-gamma (0 <= gamma < 1) by using certain generalized q integral operator. We explore geometric interpretation of the functions in this class by connecting it with conic domains. We also investigate q sufficient coefficient condition, q-Fekete-Szego inequalities, q-Bieberbach De Branges type coefficient estimates and radius problem for functions in this class. We conclude this paper by introducing an analogous subclass of k-uniformly convex functions of order-gamma by using the generalized q-integral operator. We omit the results for this new class because they can be directly translated from the corresponding results of our main class.Publication Assessment of Psychometric Characteristics of the Coronavirus Anxiety Scale in Patients with Preexisting Psychiatric Disorders(Taylor & Francis, 2022) Karahamet, Elif; Angın, Ülkem; Yılmaz, Onat; DENİZ, DERYA; Konuk, NumanThis study aimed to evaluate the psychometric characteristics of the Turkish version of the CAS in a Turkish psychiatric outpatient setting. A total of 198 patients with a preexisting psychiatric disorder completed the CAS scale. The scale's validity and reliability were evaluated using convergent and concurrent validity, internal consistency, exploratory and confirmatory factor analyses, and ROC analysis. The Turkish version of CAS might help physicians assess the COVID-19 associated anxiety in patients with psychiatric comorbidities.Publication The Association of Child Abuse Experiences and Intolerance of Uncertainty in Young Adults(Routledge, 2023) Dirican, Ayşe Hatun; Kozak, Ekin Doğa; Kavakcı, Önder; SÖNMEZ, BERNAObjective: Drawing upon the identity disruption model, we investigated the association between child abuse experiences (emotional, physical, and sexual) and intolerance of uncertainty. We also addressed demographic differences in uncertainty intolerance in this study. Methods: Using online survey questionnaires, we collected data from a sample of 302 young adults in Turkey. The data were analyzed using confirmatory factor analysis, structural equation modeling, one-way analysis of variance, and independent samples t-test. Results: The results showed that of the three types of child abuse analyzed, only emotional abuse was significantly and positively associated with intolerance of uncertainty. In contrast, age was negatively associated with intolerance of uncertainty. Regarding demographic differences, we found that the level of intolerance of uncertainty differed based on young adults’ gender, psychiatric diagnosis, and education. Specifically, our findings indicated that intolerance of uncertainty is significantly higher in females compared to males. It is also significantly higher in young adults with a diagnosis for psychiatric disorders than those without. Moreover, intolerance of uncertainty is significantly higher in young adults who have a high school graduate degree than their undergraduate and graduate counterparts. We discussed how child abuse is associated with heightened intolerance of uncertainty in young adulthood as well as why demographic differences may exist in uncertainty intolerance. Conclusions: The present study expanded the existing research on the psychological consequences of childhood abuse experiences by linking child abuse to intolerance of uncertainty. Particularly, exposure to emotional abuse in early life can be a risk factor to cope with uncertainty in later life.Publication Atiprimod Triggered Apoptotic Cell Death Via Acting on PERK/eIF2 alpha/ATF4/CHOP and STAT3/NF-Kappa B axis in MDA-MB-231 and MDA-MB-468 Breast Cancer Cells(Springer, 2021) Çoker-Gürkan, Ajda; CAN, ESİN; ŞAHİN, SEMANUR; ARISAN, ELİF DAMLA; YERLİKAYA, PINAR OBAKANPurpose The constitutive activation of STAT3 through receptor tyrosine kinases triggered breast cancer cell growth and invasion-metastasis. Atiprimod impacts anti-proliferative, anti-carcinogenic effects in hepatocellular carcinoma, lymphoma, multiple myeloma via hindering the biological activity of STAT3. Dose-dependent atiprimod evokes first autophagy as a survival mechanism and then apoptosis due to prolonged ER stress in pituitary adenoma cells. The therapeutic efficiency and mechanistic action of atiprimod in breast cancer cells have not been investigated yet. Thus, we aimed to modulate the pivotal role of ER stress in atiprimod-triggered apoptosis in MDA-MB-231 and MDA-MB-468 breast cancer cells. Results Dose- and time-dependent atiprimod treatment inhibits cell viability and colony formation in MDA-MB-468 and MDA-MB-231 breast cancer cells. A moderate dose of atiprimod (2 mu M) inhibited STAT3 phosphorylation at Tyr705 residue and also suppressed the total expression level of p65. In addition, nuclear localization of STAT1, 3, and NF-kappa B was prevented by atiprimod exposure in MDA-MB-231 and MDA-MB-468 cells. Atiprimod evokes PERK, BiP, ATF-4, CHOP upregulation, and PERK (Thr980), eIF2 alpha (Ser51) phosphorylation's. However, atiprimod suppressed IRE1 alpha-mediated Atg-3, 5, 7, 12 protein expressions and no alteration was observed on Beclin-1, p62 expression levels. PERK/eIF2 alpha/ATF4/CHOP axis pivotal role in atiprimod-mediated G1/S arrest and apoptosis via Bak, Bax, Bim, and PUMA upregulation in MDA-MB-468 cells. Moreover, atiprimod renders MDA-MB-231 more vulnerable to type I programmed cell death by plasmid-mediated increased STAT3 expression. Conclusion Atiprimod induced prolonged ER stress-mediated apoptosis via both activating PERK/eIF2 alpha/ATF4/CHOP axis and suppressing STAT3/NF-kappa B transcription factors nuclear migration in TBNC cells.Publication Auxiliary Differential Diagnosis of Schizophrenia and Phases of Bipolar Disorder Based on the Blood Serum Raman Spectra(Wiley, 2020) ILDIZ, GÜLCE ÖĞRÜÇ; Bayari, Sevgi; Aksoy, Umut M.; Yorguner, Neşe; Bulut, Hüseyin; Yılmaz, Sultan S.; Halimoğlu, Gökhan; Kabuk, Hayrunnisa Nur; YAVUZ, GİZEM; Fausto, RuiSchizophrenia (SZ) and bipolar disorder (BP) are severe psychiatric disorders that are characterized by an extensive spectrum of symptoms and affect approximately 2% of the world population. BP exhibits three well-distinct phases, which are classified as manic and depressive episodes and euthymic phase. These disorders are of difficult differential clinical diagnosis due to the similarity of their symptoms. Diagnostic approaches for SZ and BP are based on constructed patient interviews and subjective evaluations of clinical symptoms, and there are still no molecular-based auxiliary diagnostic tools to support the clinical diagnosis. In this study, an analytical model for auxiliary differential diagnosis of SZ and BP, based on the analysis of patients' blood serum Raman spectra, is developed, which is able to account for the different BP phases and can also differentiate SZ and BP patients from healthy individuals. The model is based on a hierarchical sequence of four two-class PLS-DA steps where the Raman spectra are theX-predictor variables. It is concluded that the full 400-3,100 cm(-1)Raman spectroscopic range is a sensitive probe for the disorders, thus working as a general spectroscopic biomarker for the illnesses. The proposed methodology is reliable, fast, cheap, essentially minimal-invasive, and might be implemented easily in the clinical environment.Publication BABA Pre-Treatment Before Drought Stress Revealed Tolerance Related Proteomic Alterations in Rice(Wiley, 2022) YALÇIN, HM; MAYTALMAN, S.; İHVAN, YF; GÜMÜŞ, TAMER; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMENPublication Benchmarking the Anisotropy of Nitroxyl Radical Solvation With IR Spectroscopy(The Royal Society of Chemistry, 2024) Bras, Elisa M.; Zimmermann, Charlotte; FAUSTO, RUI; Suhm, Martin A.Two simple nitroxyl radicals, di-tert-butyl nitroxyl (DTBN) and 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) are solvated by one or two water, methanol, tert-butyl alcohol or phenol molecules. The resulting low temperature IR spectra of the vacuum-isolated microsolvates in the OH stretching range are assigned based on harmonic DFT predictions for closed shell solvent dimers and trimers and their offset from experiment, to minimise theory-guided assignment bias. Systematic conformational preferences for the first and second solvent molecule are observed, depending on the conformational rigidity of the radical. These assignments are collected into an experimental benchmark data set and used to assess the spectral predicting power of different DFT approaches. The goal is to find inexpensive computational methods which provide reliable spectral predictions for this poorly explored class of microsolvates.Publication Biotic Stress-Tolerant Plants Through Small Rna Technology(Elsevier, 2020) ÇELİK, ÖZGE; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMENWith an increasing population around the world, the rapid loss of agricultural fields shows us the urgent importance of finding solutions to develop agricultural productivity. Besides industrialization, several effectors such as abiotic and biotic factors cause losses in crop productivity. Biotic factors threaten production and transportation of products worldwide. Bacteria, fungi, viruses, and oomycetes cause losses both pre- and postharvest. It is crucial to improve biotic stress-tolerant plants to overcome reduction in plant productivity. For many years, researchers focused on understanding plant defense mechanisms. Anatomical, physiological, and molecular adaptive mechanisms were investigated for several plant species. Besides the innate immunity mechanisms, including cross-talk, among the phytohormones to manage appropriate defense mechanisms against pathogens, new generation strategies in crop improvements are widely used in plant biotechnology. Although conventional breeding has importance in breeding new varieties, new technologies increase the possibility of success. Recently, new combinations of technologies have been proven effective to develop new cultivars. Small RNA technology is one of the developing crop improvement technologies relying on regulating specific genes together with their sequence identity. In this chapter, we focus on the small RNA technologies used in improvement of biotic stress-tolerant plants.Publication Blood Serum-Infrared Spectra-Based Chemometric Models for Auxiliary Diagnosis of Autism Spectrum Disorder(Elsevier, 2021) ILDIZ, GÜLCE ÖĞRÜÇ; Bayarı, Sevgi; Yorguner, Neşe; Fausto, RuiThis chapter focuses on the use of chemometric models developed from infrared (IR) spectroscopic data of blood serum as an auxiliary tool for autism spectrum disorder (ASD) diagnosis. In the introductory sections the fundamentals of IR spectroscopy are shortly reviewed and brief descriptions of the different chemometric methods used in the case study described in the last section of the chapter are presented. The last section deals with the application of the described strategy to the diagnosis of ASD in children and adolescents. © 2021 Elsevier Inc. All rights reserved.Publication Bound on Hankel Determinants H(2)4 (F) and H(3)4 (F) for Lemniscate Starlike Functions(Honam Mathematical Soc., 2023) Kumar, Sushil; Rai, Pratima; ÇETİNKAYA, ASENAWe determine the upper bounds on fourth order Hankel de-terminants H4(2) (f) and H(3) 4 (f) for the class S*L of lemniscate starlike functions defined on the open unit disk which was introduced by Sok ' o l and Stankiewicz in [17].Publication Briot-Bouquet Differential Subordinations for Analytic Functions Involving the Struve Function(MDPI, 2022) ÇETİNKAYA, ASENA; Cotirla, Luminita-IoanaWe define a new class of exponential starlike functions constructed by a linear operator involving normalized form of the generalized Struve function. Making use of a technique of differential subordination introduced by Miller and Mocanu, we investigate several new results related to the Briot-Bouquet differential subordinations for the linear operator involving the normalized form of the generalized Struve function. We also obtain univalent solutions to the Briot-Bouquet differential equations and observe that these solutions are the best dominant of the Briot-Bouquet differential subordinations for the exponential starlike function class. Moreover, we give an application of fractional integral operator for a complex-valued function associated with the generalized Struve function. The significance of this paper is due to the technique employed in proving the results and novelty of these results for the Struve functions. The approach used in this paper can lead to several new problems in geometric function theory associated with special functions.Publication Cesaro Vector Lattices and Their Ideals of Finite Elements(Springer, 2023) GÖNÜLLÜ, UĞUR; Polat, Faruk; Weber, Martin R. R.For the Cesaro matrix C = (c(nm))(n,m?N), where c(nm) = (1)/(n), if n = m and c(nm) = 0 otherwise, the Cesaro sequence spaces ces(0), ces(p) (for 1 < p < 8) and cesoo are defined. These spaces turn out to be real vector lattices and with respect to a corresponding (naturally introduced) norm they are all Banach lattices, and so possess (or not possess) some interesting properties. In particular, the relations to their generating ideals c(0), t(p) and t(8) are investigated. Finally the ideals of all finite, totally finite and selfmajorizing elements in ces(0), ces(p) (for 1 < p <8) and ces(8) are described in detail.Publication Circulating MicroRNA Expression Profiles to Identify a Potential Link Between Prostate Cancer and Obesity(Elsevier, 2022) Arışan, Serdar; KILBAŞ, PELİN ÖZFİLİZ; RENCÜZOĞULLARI, ÖZGE; Ünsal, Narcin Palavan; Çoker-Gürkan, Ajda; Uysal-Onganer, Pınar; ARISAN, ELİF DAMLA; YERLİKAYA, PINAR OBAKANEffective diagnostic methods are needed to apply appropriate treatment strategies in patients with aggressive prostate cancer. From this point of view, risk factors that cause prostate cancer or its aggressiveness should be considered. Obesity is a critical risk factor for triggering prostate cancer's metastatic properties. microRNAs are used as biomarkers in diagnosing cancer and obesity depending on their tissue-specific expression patterns. This study investigates the role of obesity in the metastatic profile of prostate cancer depending on the differential expression signatures of selected miRNAs in prostate cancer and obese patients. The roles of miR-100, miR-141 and miR-145 in prostate cancer and obesity are partially known. However, their potential to become circular biomarkers in the blood is not elucidated. There is no previous data on miR-4463 and miR-653 on prostate cancer and obesity association. In this study, the blood samples were taken and obtained serum from 69 patients of 6 subgroups that consisted of one healthy group and five unhealthy groups based on their different prostate cancer or obesity levels. Five selected miRNA expression analyses (miR-100, miR-141, miR-145, miR-4463, and miR-653) were performed through total RNA isolation, which was confirmed via synthetic cel-miR-39 miRNA. Quantitative Real-Time PCR analyzed the expression levels of selected miRNAs. Data analysis was performed via normalising target miRNA expression levels with cel-miR-39. In this study, we found that the relationship between prostate cancer and obesity was investigated at the molecular level. It was suggested that target miR-100 could be a promising biomarker for non-obese and aggressive prostate cancer patients. miR-145 is a more potential biomarker than miR-141 for non-aggressive and non-obese patients. miR-4463 can be used to predict more prostate cancer patients than obese patients. Lastly, miR-653 can be a biomarker for non-aggressive prostate cancer cells.Publication Co-Chaperone Bag-1 Plays a Role in the Autophagy-Dependent Cell Survival Through Beclin 1 Interaction(MDPI, 2021) Türk, Miray; Tatlı, Özge; Alkan, Hamza Furkan; KILBAŞ, PELİN ÖZFİLİZ; Alkurt, Gizem; Dinler Doğanay, GizemExpression levels of the major mammalian autophagy regulator Beclin 1 and its interaction with Bcl-2 regulate the switch between autophagic cell survival and apoptotic cell death pathways. However, some of the regulators and the precise mechanisms of these processes still remain elusive. Bag-1 (Bcl-2 associated athanogene-1), a member of BAG family proteins, is a multifunctional pro-survival molecule that possesses critical functions in vital cellular pathways. Herein, we report the role of Bag-1 on Bcl-2/Beclin 1 crosstalk through indirectly interacting with Beclin 1. Pull-down experiments suggested a molecular interaction between Bag-1 and Beclin 1 in breast cancer cell lines. On the other hand, in vitro binding assays showed that Bag-1/Beclin 1 interaction does not occur directly but occurs through a mediator molecule. Bag-1 interaction with p-Beclin 1 (T119), indicator of early autophagy, is increased during nutrient starvation suggesting involvement of Bag-1 in the autophagic regulation. Furthermore, CRISPR/Cas9-mediated Bag-1 knock-out in MCF-7 cells hampered cell survival and proliferation and resulted in decreased levels of total LC3 under starvation. Collectively, we suggest that Bag-1 modulates cell survival/death decision through maintaining macroautophagy as a component of Beclin 1-associated complexes.Publication Coefficient Estimates for Bi-Univalent Functions in Connection with Symmetric Conjugate Points Related to Horadam Polynomial(MDPI, 2020) Aydoğan, S. Melike; Karahüseyin, ZelihaIn the current study, we construct a new subclass of bi-univalent functions with respect to symmetric conjugate points in the open disc E, described by Horadam polynomials. For this subclass, initial Maclaurin coefficient bounds are acquired. The Fekete-Szego problem of this subclass is also acquired. Further, some special cases of our results are designated.Publication Coefficient Inequalities for Certain Starlike and Convex Functions(Hacettepe University, 2022) Çetinkaya, Asena; Kumar, SushilIn this paper, we consider two Ma-Minda-type subclasses of starlike and convex functions associated with the normalized analytic function phi(Ne)(z) = 1 + z - z3/3 that maps an open unit disk onto the Nephroid shaped bounded domain in the right-half of the complex plane. We investigate convolution and quasi-Hadamard product properties for the functions belonging to such classes. In addition, we compute best possible estimates on third order Hermitian-To eplitz determinant and non-sharp estimates on certain third order Hankel determinants for the starlike functions associated with the interior region of Nephroid.Publication Comparison of COVID-19 Laboratory Diagnosis by Commercial Kits: Effectivity of RT-PCR to the RT-LAMP(Wiley, 2022) ARTIK, YAKUP; Coşgun, Alp B.; Cesur, Nevra P.; Hızel, Nedret; Uyar, Yavuz; Sur, Haydar; AYAN, ALPCoronavirus disease 2019 or COVID-19 caused by novel coronavirus/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic that has emerging global effects and requires rapid and reliable diagnostic testing. Quantitative reverse transcription-polymerase chain reaction (q-RT-PCR) is the gold standard method for SARS-CoV-2 detections. On the other hand, new approaches remedy the diagnosis difficulties gradually. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) as one of these novel approaches may also contribute to faster and cheaper field-based testing. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 min and to compare the effectiveness of LAMP to the q-RT-PCR. The 30 randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values was tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 [SARS-CoV-2] LAMP Assay, the QIAseq DIRECT SARS-CoV-2 kit, Biospeedy SARS-CoV-2 Variant Plus kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia Technologies GenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (positivity 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device were 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). On the fifth day, the samples were studied in the Inovia device and the respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in the Qiagen kit (positivity 63.3%). When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity 60%) on the fifth day. SARS-CoV-2 test studies will contribute to a proactive approach to the development of rapid diagnosis systems. The LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry.