Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Letter Citation - WoS: 1Citation - Scopus: 1Evaluating Ethanol Concentrations Against Staphylococcus Spp: a Proposal for Improving Nosocomial Bacteria Control(Elsevier, 2024) Soyer, Ferda; Özdemir, Özgün Öykü; Polat, Bengi; Ekenel, Nil HazalDear Editor, Nosocomial infections originating from commonly encountered pathogenic bacteria, notably Staphylococcus species, persist as a prominent global public health issue. This phenomenon exerts consequential impacts on both the well-being of patients and the healthcare personnel within hospital environments. Hospital-acquired infections from common bacteria like Staphylococcus remain a global public health concern. The European Centre for Disease Prevention and Control reports prevalence rates of 4.5% in the USA and 7.1% in Europe [1]. An estimated 8.9 million healthcare-associated infections occur annually in European hospitals and long-term care facilities [1]. According to the World Health Organization, although 10% of patients get healthcare-associated infections, at least a 30% reduction can be achieved through adequate infection prevention and control [2]. The efficacy of disinfection methodologies employed in healthcare institutions assumes critical significance in mitigating this threat.Article Blank Frame and Intensity Variation Distortion Detection and Restoration Pipeline for Phase-Contrast Microscopy Time-Lapse Images(Aves, 2024) Ucar, Mahmut; Iheme, Leonardo O.; Onal, Sevgi; Pesen-Okvur, Devrim; Yalcin-Ozuysal, Ozden; Toreyin, Behcet U.; Unay, DevrimIn this study, we propose a preprocessing pipeline for the detection and correction of distorted frames in time-lapse images obtained from phase-contrast microscopy. The proposed pipeline employs the average intensities of frames as a foundational element for the analysis. In order to evaluate the degree of correction required for intensity variance, a normalization technique is applied to the difference between the average intensity of a specific frame and the median average intensity of all frames within the study. Our restoration method increases the histogram similarity between the distorted and non-distorted frames, preserves trans-passing pixels in regions of interest, and mitigates the development of additional distortions. The efficacy of the proposed method was evaluated using 15 395 time-lapse image frames from 27 experiments using our own dataset and 830 time-lapse images from four different experiments obtained from the cell tracking challenge. The results of the validation demonstrate a high degree of numerical and visual accuracy of the proposed pipeline.Article Citation - WoS: 2Citation - Scopus: 2Gas Phase Fragmentation Behavior of Proline in Macrocyclic B7 Ions(American Chemical Society, 2023) Taşoğlu, Çağdaş; Arslanoğlu, Alper; Yalçın, TalatThefragmentation characteristics of b (7) ionsproduced from proline-containing heptapeptides have been studiedin detail. The study has utilized the following C-terminally amidatedmodel peptides: PA(6), APA(5), A(2)PA(4), A(3)PA(3), A(4)PA(2), A(5)PA, A(6)P, PYAGFLV, PAGFLVY, PGFLVYA, PFLVYAG,PLVYAGF, PVYAGFL, YPAGFLV, YAPGFLV, YAGPFLV, YAGFPLV, YAGFLPV, YAGFLVP,PYAFLVG, PVLFYAG, A(2)PXA(3), and A(2)XPA(3) (where X = C, D, F, G, L, V, and Y, respectively). The resultshave shown that b (7) ions undergo head-to-tailcyclization and form a macrocyclic structure. Under the collision-induceddissociation (CID) condition, it generates nondirect sequence ionsregardless of the position of the proline and the neighboring aminoacid residues. This study highlights the unusual and unique fragmentationbehavior of proline-containing heptapeptides. Following the head-to-tailcyclization, the ring opens up and places the proline residue in theN-terminal position while forming a regular oxazolone form of b (2) ions for all peptide series. Then, the fragmentationreaction pathway is followed by the elimination of proline with itsC-terminal neighbor residue as an oxazolone (e.g., PXoxa) for all proline-containing peptide series.Article Citation - WoS: 2Citation - Scopus: 3Investigating the Potential Therapeutic Role of Targeting Stat3 for Overcoming Drug Resistance by Regulating Energy Metabolism in Chronic Myeloid Leukemia Cells(Mashhad University of Medical Sciences, 2022) Tezcanlı Kaymaz, Burçin; Günel, Nur Selvi; Söğütlü, Fatma; Özateş Ay, Neslihan Pınar; Baran, Yusuf; Gündüz, Cumhur; Biray Avcı, ÇığırObjective(s): STATs are one of the initial targets of emerging anti-cancer agents due to their regulatory roles in survival, apoptosis, drug response, and cellular metabolism in CML. Aberrant STAT3 activity promotes malignancy, and acts as a metabolic switcher in cancer cell metabolism, contributing to resistance to TKI nilotinib. To investigate the possible therapeutic effects of targeting STAT3 to overcome nilotinib resistance by evaluating various cellular responses in both sensitive and nilotinib resistant CML cells and to test the hypothesis that energy metabolism modulation could be a mechanism for re-sensitization to nilotinib in resistant cells. Materials and Methods: By using RNAi-mediated STAT3 gene silencing, cell viability and proliferation assays, apoptotic analysis, expressional regulations of STAT mRNA transcripts, STAT3 total, pTyr705, pSer727 protein expression levels, and metabolic activity as energy metabolism was determined in CML model K562 cells, in vitro. Results: Targeting STAT3 sensitized both parental and especially nilotinib resistant cells by decreasing leukemic cell survival; inducing leukemic cell apoptosis, and decreasing STAT3 mRNA and protein expression levels. Besides, cell energy phenotype was modulated by switching energy metabolism from aerobic glycolysis to mitochondrial respiration in resistant cells. RNAi-mediated STAT3 silencing accelerated the sensitization of leukemia cells to nilotinib treatment, and STAT3-dependent energy metabolism regulation could be another underlying mechanism for regaining nilotinib response. Conclusion: Targeting STAT3 is an efficient strategy for improving the development of novel CML therapeutics for regaining nilotinib response, and re-sensitization of resistant cells could be mediated by induced apoptosis and regulation in energy metabolism.Article Citation - Scopus: 2Qtl Mapping of Broomrape (orobanche Cumana Wallr.) Resistance in Sunflower (helianthus Annuus L.) Using Gbs-Snps(Society of Field Crops Science, 2021) Akköse Baytar, Asena; Çelik, İbrahim; Doğanlar, Cafer; Frary, Anne; Doğanlar, SamiBroomrape is one of the most important biotic stresses causing serious yield reductions in sunflower. Control of this parasitic plant is difficult and physical and chemical strategies are usually insufficient. Therefore, introduction of genetic resistance to broomrape in sunflower is a key breeding goal. Breeding efforts on broomrape resistance have been conducted for decades, however, new broomrape races, such as race F, have emerged and rapidly evolved to be more aggressive and devastating. Although a few quantitative trait loci (QTLs) were identified for race F resistance, none of these loci are suitable for marker assisted selection because of their small phenotypic effects. In the present study, three major QTLs for broomrape race F resistance were identified on LG7, LG11 and LG12 using a high density SNP map constructed with the genotyping by sequencing approach in an intraspecific F2 population. The population consisted of 300 individuals derived from a cross between susceptible Helianthus annuus cv. RHA 436 as the recipient parent and resistant H. annuus cv. H08 M1 as the donor parent. Breeder-friendly SNP-based cleaved amplified polymorphic sequence markers were developed for the QTLs. The QTLs and CAPS markers identified in this study will be valuable molecular genetic tools for sunflower breeding.Editorial Citation - Scopus: 1Lessons From a Ten-Year Journey: Building a Student-Driven Computational Biology Society Across Turkey(F1000 Research, 2022) Kaya, Yasin; Karakulak, Tülay; Saylan, Cemil Can; Gür, E. Ravza; Tatlıdil, Engin; Güleşen, Sevilay; Betül Dinçaslan, Fatma; Dönertaş, Handan MelikeThe Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics.Article Citation - WoS: 15Citation - Scopus: 16The Usability of Juniperus Virginiana L. as a Biomonitor of Heavy Metal Pollution in Bishkek City, Kyrgyzstan(Taylor & Francis, 2015) Kurmanbekova, Gülbübü; Severoğlu, Zeki; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yalçın, İbrahim Ertuğrul; Kaşoğlu, GültenUncontrolled and unplanned urbanization and industrialization due to increase of population and rapid industrial development have created severe environmental problems in Kyrgyzstan during the last few decades. In this study, Juniperus virginiana, a dioecious species, was employed in order to make assessment of the heavy metal pollution rate in the area and of the heavy metal pollution impact on the mineral nutrient status of the plant. For this study, leaf (washed and unwashed) and bark samples of J. virginiana, and its co-located soil samples were collected from eight different stations, all in the capital of Kyrgyzstan, Bishkek, in 2012 vegetation period. The standard procedures were used and the determinations of heavy metal and nutrient element contents (Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Pb and Zn) in all samples were done using inductively coupled plasma-optical emission spectroscopy. According to our measurements, J. virginiana was found to be capable of accumulating a considerable amount of metals and the mineral nutrient uptake pattern was altered because of metal deposition in the plant, which showed a contamination risk in the area.Article Citation - WoS: 20Citation - Scopus: 19Using the Turkish Red Pine Tree To Monitor Heavy Metal Pollution(HARD, 2020) Yalçın, Ertuğrul; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yarcı, CelalTurkish red pine is an evergreen tree species widely distributed in the Aegean and Mediterranean regions in Turkey. In the present work, the heavy metal pollution level in Istanbul was investigated using Turkish red pine as a biomonitor. For determining heavy metal concentrations (Cd, Co, Cr, Mn, Ni and Pb) in leaf (unwashed and washed) and bark samples of Turkish red pine and its co-located soil samples we used ICP-OES. Additionally, particulate matter profiles of the research areas were investigated. The samples were collected from 5 different localities: 4 from the Bosporus region (Yildiz Grove, Fethi Pasha Grove, Baltalimani Grove and Mihrabad Grove) and one from Prince Island, also known as Buyukada (as control). According to our measurements, the highest heavy metal accumulations (in mg kg(-1) DW) in plant part samples were measured between 1.526 +/- 0.012 and 1.639 +/- 0.015 for Cd, 0.543 +/- 0.007 and 0.600 +/- 0.009 for Co, 5.110 +/- 0.064 and 5.648 +/- 0.072 for Cr, 9.347 +/- 0.105 and 10.331 +/- 0.111 for Mn, 7.483 +/- 0.091 and 8.271 +/- 0.096 for Ni, and 13.848 +/- 0.159 and 14.950 +/- 0.167 for Pb, while the highest heavy metal accumulations (in mg kg(-1) DW) in soil samples were measured between 1.813 +/- 0.021 and 1.974 +/- 0.029 for Cd, 6.326 +/- 0.082 and 6.992 +/- 0.091 for Co, 22.017 +/- 0.284 and 23.685 +/- 0.301 for Cr, 268.333 +/- 3.153 and 297.361 +/- 3.529 for Mn, 15.194 +/- 0.176 and 16.792 +/- 0.193 for Ni, and 68.778 +/- 0.715 and 74.514 +/- 0.883 for Pb. The highest outdoor particulate matter levels (in mu g/m(3)) in research areas were also determined as 27.103 for fine (PM2.5) and 67.792 for coarse (PM10) aerosols. The findings revealed that Turkish red pine could accumulate noteworthy amounts of heavy metals.Article Thrips parazitoiti Ceranisus (Hymenoptera: Eulophidae) cinsinin morfolojik yapı ve 28S D2 rDNA temelinde Türkiye’deki güncel taksonomik durumları(Türkiye Entomoloji Derneği, 2010) Doğanlar, Oğuzhan; Doğanlar, Mikdat; Frary, AnneÇalışma ile Mayıs 2006 ile Mayıs 2007 tarihleri arasında Güneydoğu Anadolu Bölgesi ve Akdeniz Bölgesi’nin doğusunda bulunan Ceranisus (Hymenoptera: Eulophidae) cinsi ve benzer diğer cinslerin genetik analizleri yapılarak, bu verilerin diğer thrips parazitoitlerinin morfolojik yapılarıyla mukayese edilip, türlerin kesin teşhislerinin yapılması amaçlanmıştır. Bu kapsamda, Hatay, Gaziantep, Adıyaman ve Şanlıurfa’da 38 farklı noktada örnekleme yapılmış ve 20 örnekleme noktasında toplam 143 adet (30 erkek; 113 dişi) Ceranisus cinsine giren tür toplanmıştır. Populasyon morfolojik özelliklerine göre 13 farklı gruba ayrılmıştır. Bu türlerin filogenetik ilişkileri DNA dizileri kullanılarak verilmiştir. Toplam 15 tür 28S D2 ribosomal DNA bölgesi kullanılarak analiz edilmiştir. Analiz sonucunda morfolojik olarak ayrılan 13 farklı tür grubundan 3 tanesinin genetik olarak farklı olduğu görülmüştür. Diğer türlerden ise 4 adetinin C. nr. lepidotus grubu oluşturdukları, 5 adet C. nr. bozovaensis’in ise kendi aralarında 2 farklı grup oluşturdukları belirlenmiştir. Sonuç olarak 3 adet yeni Ceranisus türü, bunun haricinde 3 adet farklı türü oluşturabilecek popülasyon genetik olarak belirlenmiştir.Conference Object Effects of Hesperidin on Non-Small Cell Lung Cancer Cells(International Institute of Anticancer Research, 2014) Bireller, Elif Sinem; Cincin, Zeynep Birsu; Ünlü, Miray; Kıran, Bayram; Baran, Yusuf; Çakmakoğlu, BediaBackground: Hesperidin, a glycoside flavonoid that is found in citrus fruits, and the mechanisms of hesperidin-induced apoptosis are not well understood. In this study, we aimed to investigate the cytotoxic and apoptotic aspect of hesperidin induction in lung cancer.