Fen Edebiyat Fakültesi / Faculty of Letters and Sciences
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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 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 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 Epibrassinolide-Induced Autophagy Occurs in an Atg5-Independent Manner Due to Endoplasmic Stress Induction in MEF Cells(Springer, 2020) Adacan, Kaan; YERLİKAYA, PINAR OBAKAN; Çoker-Gürkan, Ajda; Kaya, Resul İsmail; Palavan-Ünsal, Narcin; ARISAN, ELİF DAMLAEpibrassinolide (EBR), a polyhydroxysteroid belongs to plant growth regulator family, brassinosteroids and has been shown to have a similar chemical structure to mammalian steroid hormones. Our findings indicated that EBR could trigger apoptosis in cancer cells via induction of endoplasmic reticulum (ER) stress, caused by protein folding disturbance in the ER. Normal cells exhibited a remarkable resistance to EBR treatment and avoid from apoptotic cell death. The unfolded protein response clears un/misfolded proteins and restore ER functions. When stress is chronic, cells tend to die due to improper cellular functions. To understand the effect of EBR in non-malign cells, mouse embryonic fibroblast (MEF) cells were investigated in detail for ER stress biomarkers, autophagy, and polyamine metabolism in this study. Evolutionary conserved autophagy mechanism is a crucial cellular process to clean damaged organelles and protein aggregates through lysosome under the control of autophagy-related genes (ATGs). Cells tend to activate autophagy to promote cell survival under stress conditions. Polyamines are polycationic molecules playing a role in the homeostasis of important cellular events such as cell survival, growth, and, proliferation. The administration of PAs has been markedly extended the lifespan of various organisms via inducing autophagy and inhibiting oxidative stress. Our data indicated that ER stress is induced following EBR treatment in MEF cells as well as MEF Atg5(-/-) cells. In addition, autophagy is activated following EBR treatment by targeting PI3K/Akt/mTOR in wildtype (wt) cells. However, EBR-induced autophagy targets ULK1 in MEF cells lacking Atg5 expression. Besides, EBR treatment depleted the PA pool in MEF cells through the alterations of metabolic enzymes. The administration of Spd with EBR further increased autophagic vacuole formation. In conclusion, EBR is an anticancer drug candidate with selective cytotoxicity for cancer cells, in addition the induction of autophagy and PA metabolism are critical for responses of normal cells against EBR.Publication Examination of Fatty Acid Metabolism and Induction of Epithelial-Mesenchymal Transition Pathway via Modulation of miR-33a Levels in Caki-1 and Caki-2 Renal Cell(Wiley, 2022) İNCE, İ.; KALABALIKOĞLU, E.; ŞAHİN, BURCU AYHAN; KILBAŞ, PELİN ÖZFİLİZ; RENCÜZOĞULLARI, ÖZGEPublication Examining the Relationship of Diabetes-Related Cytokine Levels and EMT in STAT5-overexpressed Panc-1 and MiaPaCa-2 Pancreatic Cancer Spheroid Models in Response to Celastrol Treatment(WİLEY, 2022) RENCÜZOĞULLARI, ÖZGE; SARIKAYA, E.N.; KAHYA, B.Publication An Exploration of the Subtypes of Male Youth Adjudicated for Sex Offenses: A Latent Class Analysis Based on Personal, Offense, and Victim Characteristics(Sage Publications Inc., 2022) Büker, Hasan; Cohen, Achraf; ERBAY, AYHANThis study intended to explore possible variations among youth adjudicated for sexual offenses based on personal criminogenic factors, offense, and victim characteristics. Utilizing a data set collected from the juvenile court files in Turkey (n = 460), the Latent Class Analysis revealed that the study sample included three different subgroups with distinct features: "non-delinquent, peer victim-targeting," "non-delinquent, younger victim-targeting," and "delinquent, versatile" youth adjudicated for sex offenses. The first two of these groups were similar in terms of having low levels of delinquency, while the third group included the lowest number of youth with significantly broad delinquent activity patterns. These findings were in line with the results of previous studies, and the implications were discussed for future research and policy development.Publication Heavy Metal Stress-Responsive Phyto-miRNAs(Springer Science and Business Media B.V., 2020) ÇELİK, ÖZGE; AYAN, ALP; MERİÇ, SİNAN; ATAK, ÇİMENHeavy metal stress is a leading abiotic stress factor in the twenty-first century as a reflection of industrial developments and extensive urbanization. Plants adopt several adaptation mechanisms to cope with deleterious effects of heavy metal stress. Biosynthesis of amino acids/organic acids, phytochelatins (PCs), metallothioneins (MTs), heat-shock proteins (HSPs), metal chelators, chaperons, ABC-type transporters, and CDF family metal transporters are among the heavy metal binding or transporting mechanisms in plants. This chapter emphasizes phyto-miRNAs related to these tolerance mechanism pathways. Moreover, transcription factors which are targeted by heavy metal-related phyto-miRNAs are also summarized under the effect of various heavy metals due to their intertwined regulatory mechanisms.Publication The Importance of Polymers in Medicine and their FTIR and Raman Spectroscopic Investigations(IGI Global, 2023) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Polymers are macromolecules with a very high molecular weight that are formed as a result of one or more small molecules bonding to each other, typically by covalent bonds. The concept of macromolecules consisting of many repeating units are published in the article titled "Uber Polymerization," which was first published in 1920 by Hermann Staudinger. The idea of polymers, which have been in our lives for a long time, has thus become an important field of study. Polymers are commonly used in tissue engineering because of their properties such as biocompatibility and biodegradability. In addition, polymers have a wide range of applications in tissue regeneration, drug delivery, and wound healing. Polymers have varying structural properties based on their backbone structure, molecular weight, and crystallinity. For this cause, a great deal of study in the medicine has been based on this category of materials. This workfocuses on the importance of polymers in the medicine, 3D printed polymer composites and Fourier transform infrared, and Raman spectroscopic investigations of polymeric structures.Publication Investigation of the Effect of STAT3 Inhibition on Apoptotic Process Associated with JAK/STAT Signaling Pathway in A-498 and ACHN Renal Carcinoma Cells(Wiley, 2022) YILDIZHAN, K. Y.; AYDIN, Y. E.; KILBAŞ, PELİN ÖZFİLİZ; ŞAHİN, BURCU AYHAN; RENCÜZOĞULLARI, ÖZGEPublication A New Copy of Baki's Divan and Baki's Poems That Are Not in Divan Publications(Ahmet Yesevi Üniversitesi, 2023) KÖKSAL, MEHMET FATİHThe most brilliant period of classical Turkish poetry was the 16th century; the science, art and literature center of the 16th century was Istanbul; and the greatest poet of the period in Istanbul was Baki. Baki was known as "the sultan of poets " in his time. His poems , and especially his ghazals, were recorded in hundreds of poetry collections (mecmua) besides the manuscripts of his Divan. Baki's unpublished poems may be found in mostly poetry collections and in some Divan copies. In a copy of Bakis' Divan, which is in the personal library of M. Fatih Koksal, there are 20 unknown poems of Baki, 6 of which are ghazals, 1 of which are kit'a, and 13 of which are matla-mufred. Another interesting feature of the Koksal's copy is that 24 imitations (nazire) of 17 poets, some of which are not mentioned in the sources, were recorded in the margins. In this article, after evaluating the existence of Baki's poems that are included in some poetry collections but not in Divan copies, the said Divan copy will be introduced and the transcripted text of 20 unpublished poems will be published. The first couplets (matla') of the poems that are not found in the divan copies but have been brought to light by some publications will also be included.Publication A New Topology Via a Topology(American Institute of Physics Inc., 2022) DAĞCI, FİKRİYE İNCE; Çakallı, HüseyinIn this extended abstract, we modify the definition of h-open set introduced in [1] by F. Abbas who neglects that the set of all h-open sets is a topology, and we show that the union of any family of h-open subsets of X is h-open that ensures that the set of all h-open subsets of a topological space (X, τ) forms a topology which is finer than τ, where a subset A of a topological space (X, τ) is said to be h-open if A ⊆ Int(A ∪ U) for every non-empty subset U of X such that U ∈ τ. We also give continuity type theorems. © 2022 American Institute of Physics Inc.. All rights reserved.Publication On Group Analysis of Optimal Control Problems in Economic Growth Models(American Institute of Mathematical Sciences, 2020) POLAT, GÜLDEN GÜN; Özer, TeomanThe optimal control problems in economic growth theory are analyzed by considering the Pontryagin's maximum principle for both current and present value Hamiltonian functions based on the theory of Lie groups. As a result of these necessary conditions, two coupled first-order differential equations are obtained for two different economic growth models. The first integrals and the analytical solutions (closed-form solutions) of two different economic growth models are analyzed via the group theory including Lie point symmetries, Jacobi last multiplier, Prelle-Singer method,_-symmetry and the mathematical relations among them.Publication The Petrifying, Apotropaic Gaze and Matrixial Vulva of Medusa, alongside Genital Display Figures(Indiana University Press, 2023) ALBAN, GILLIAN MARY ELIZABETHThis review of ten articles, books, and chapters on the mythic Medusa and genital display figures illustrates Medusa's petrifying and apotropaic gaze and her engulfing vulva, or eye blazoning her matrixial force, as her severed head demonstrates her abiding pro-creative, indomitable force. Through a history of women held under scrutiny while feared by patriarchy, with men projecting their own fear of castration onto them, the Medusa figure emerges as stun-ningly uncastrated, asserting her force and returning her stony gaze in the reflexive action pivotal to this myth. Objectified under the male gaze, her vulva faces the viewer, her inspirational force born through the birth of Pegasus even as she is crushed in rape and death. The mythic Medusa and vulva display women persistently retain their hold on the male unconscious in rising above castiga-tion, asserting their amazing procreative force over life and death, enabled through Medusa's stunning tale and transfixing gaze.Publication Polymorphism in 1-Methylhydantoin: Investigation by Periodic DFT Calculations and Characterization of the Third Polymorph(Royal Society of Chemistry, 2020) Nogueira, Bernardo A.; Milani, Alberto; ILDIZ, GÜLCE ÖĞRÜÇ; Paixão, José A.; Castiglioni, Chiara; Fausto, RuiIn previous studies [Puszyńska-Tuszkanow et al. Polyhedron, 2011, 30(12), 2016; Nogueira et al. J. Phys. Chem. A, 2014, 118(31), 5994; Nogueira et al., J. Mol. Struct., 2017, 1148, 111], two different polymorphs of 1-methylhydantoin (1-MH, C4H6N2O2) were identified (forms I and II) and characterized using infrared and Raman spectroscopies, as well as by X-ray diffraction. In this work, a new polymorph of the compound (form III) is described. The new polymorph was characterized spectroscopically and its structure was determined for the first time by single crystal X-ray diffraction. Very interestingly, the crystal of polymorph III was found to exhibit a high-Z′ (Z′ = 3) asymmetric unit and 12 molecules in the unit cell (Z = 12), which contrasts with the simpler crystal structures found previously for forms I and II (Z = 4; Z′ = 1). Besides, a thorough study of the polymorphism of 1-MH was performed with the help of state-of-the-art first principles fully periodic calculations of the structure, as well as infrared and Raman spectra of the different polymorphs of the compound. Marker-bands in the infrared and Raman spectra of the polymorphs are proposed for fast spectroscopic identification of the polymorphs.Publication Proinflammatory Cytokine Profile is Critical in Autocrine GH-Triggered Curcumin Resistance Engulf by Atiprimod Cotreatment in MCF-7 and MDA-MB-231 Breast Cancer Cells(Springer, 2020) Çoker-Gürkan, Ajda; Özakaltun, Buse; Akdeniz, Berre-Serra; Ergen, Berfin; YERLİKAYA, PINAR OBAKAN; Akkoç, Tunç; ARISAN, ELİF DAMLAActive growth hormone (GH) signaling triggers cellular growth and invasion-metastasis in colon, breast, and prostate cancer. Curcumin, an inhibitor of NF-kappa B pathway, is assumed to be a promising anti-carcinogenic agent. Atiprimod is also an anti-inflammatory, anti-carcinogenic agent that induces apoptotic cell death in hepatocellular carcinoma, multiple myeloma, and pituitary adenoma. We aimed to demonstrate the potential additional effect of atiprimod on curcumin-induced apoptotic cell death via cytokine expression profiles in MCF-7 and MDA-MB-231 cells with active GH signaling. The effect of curcumin and/or atiprimod on IL-2, IL-4, and IL-17A levels were measured by ELISA assay. MTT cell viability, trypan blue exclusion, and colony formation assays were performed to determine the effect of combined drug exposure on cell viability, growth, and colony formation, respectively. Alteration of the NF-kappa B signaling pathway protein expression profile was determined following curcumin and/or atiprimod exposure by RT-PCR and immunoblotting. Finally, the effect of curcumin with/without atiprimod treatment on Reactive Oxygen Species (ROS) generation and apoptotic cell death was examined by DCFH-DA and Annexin V/PI FACS flow analysis, respectively. Autocrine GH-mediated IL-6, IL-8, IL-10 expressions were downregulated by curcumin treatment. Atiprimod co-treatment increased the inhibitory effect of curcumin on cell viability, proliferation and also increased the curcumin-triggered ROS generation in each GH(+) breast cancer cells. Combined drug exposure increased apoptotic cell death through acting on IL-2, IL-4, and IL-17A secretion. Forced GH-triggered curcumin resistance might be overwhelmed by atiprimod and curcumin co-treatment via modulating NF-kappa B-mediated inflammatory cytokine expression in MCF-7 and MDA-MB-231 cells.Publication The Role of the PI3K/AKT/mTOR Signaling Axis in the Decision of the Celastrol-Induced Cell Death Mechanism Related to the Lipid Regulatory Pathway in Prostate Cancer Cells(Elsevier, 2020) RENCÜZOĞULLARI, ÖZGE; Çoban, Mervenur; Sevgin, Bortecine; Çoker-Gürkan, Ajda; YERLİKAYA, PINAR OBAKAN; Palavan-Ünsal, Narcin; ARISAN, ELİF DAMLAProstate cancer is one of the leading cancer types among the male population worldwide, with high incidence and mortality rates. Celastrol is a promising bioactive component extracted from Tripterygium wilfordi. Celastrol is a multimodal agent with therapeutic advantages, with activities that affect cell proliferation, inflammation (through affecting proteotoxic stress) and cell death mechanisms such as autophagy, apoptosis and paraptosis. Celastrol alters the PI3K/AKT signaling axis to suppress the cell viability of cancer cells. Although a number of celastrol targets have been identified in cancer cells, the genomic differences in malignant cells prevent the efficacy of celastrol. Therefore, new studies are required to highlight its potential therapeutic effects in cancer cells. In this study, we investigated the therapeutic potential of celastrol in LNCaP, DU145 and PC3 prostate cancer cells. According to our results, celastrol decreased cell viability in a dose-dependent manner in the cells. LNCaP prostate cancer cells were more sensitive to celastrol treatment compared to DU145 and PC3 cells. We found that celastrol modulated PI3K/AKT/mTOR signaling to alter lipid regulatory pathways by affecting LAMP -1 and lipin-1 in PC3 cells. Although celastrol downregulated FASN in all cell lines, active mTOR signaling led to altered responses in prostate cancer cells by affecting the cellular fate decision pathways.Publication Structural and Spectral Analysis of Anticancer Active Cyclo(Ala-His) Dipeptide(Taylor & Francis Inc., 2020) Çelik, Sefa; YILMAZ, GÖZDE; Özel, Ayşen E.; AKYÜZ, SEVİMThe theoretically possible most stable conformation of the cyclic dipeptide, which has a significant anticancer activity, was examined by conformational analysis method and then by DFT calculations. With DFT calculations, cyclo(Ala-His) dipeptide was found to be more stable in boat form than in planar conformation. Moreover, conformations of the dimeric forms of the title molecule were investigated. The dimeric forms of the cyclo(Ala-His) dipeptide were created by combining two identical cyclo(Ala-His) monomers, in lowest energy configuration and as a result three energetically possible dimeric structures were obtained. The solid phase FTIR and Raman spectra of cyclo(Ala-His) have been recorded. The spectra were interpreted with the aid of quantum chemical calculations based on density functional theory, using B3LYP and wb97xd methods with 6-311++G(d,p) basis set, in order to elucidate structural and spectral properties of the investigated molecule. Experimental vibrational spectra are found to be in accord with the simulated vibrational spectra. The assignment of the vibrational modes was performed depending on the calculated potential energy distribution (PED).In slicomolecular docking of cyclo(Ala-His) was also carried out with DNA. The drug likeness and ADMET properties were analyzed for the prediction of pharmacokinetic profiles. The results revealed that the compound has the potential to be the leading molecule in the drug discovery process.Publication A Survey on the Theory of Integral and Related Operators in Geometric Function Theory(Springer, 2021) Ahuja, Om P.; ÇETİNKAYA, ASENAA brief tour of more than one hundred years of the historical development of some of the popular integral and related operators in Geometric Function Theory (GFT) is given in this article. The strengths and discovery of the methods used in these operators lie in their ability to unify a large number of diverse operators and results. We also address some of the q- analogues of the integral operators in GFT. Since there are several surveys and books in GFT, we present here only a selection of the results related to our precise objectives. © 2021, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.