WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7150

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Department: search.filters.department.İzmir Institute of Technology. Molecular Biology and GeneticsPublisher: search.filters.publisher.Taylor and Francis Ltd.

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Now showing 1 - 10 of 21
  • Article
    Citation - WoS: 37
    Mechanisms of Cellular Resistance To Imatinib in Human Chronic Myeloid Leukemia Cells
    (Taylor and Francis Ltd., 2007) Baran, Yusuf; Ural, Ali Uğur; Gündüz, Ufuk
    A major advancement in the treatment of chronic myeloid leukemia (CML) has been the development of imatinib, which has shown striking activity in the chronic phase and the accelerated phase, but less so in the blast phase of the disease. Despite high rates of hematologic and cytogenetic responses to therapy, the emergence of resistance to imatinib has been recognized as a major problem in the treatment of patients with CML. Various cellular mechanisms may be involved in the nature of cellular resistance. Increased amount of target, alteration in structure of target proteins, decreased drug uptake and increased detoxification are well-known mechanisms of resistance. On the other hand, in some cases, even if anticancer drugs reach their sites of action, bypassing drug efflux system of the cells, some cells still may survive via the dysregulation of apoptotic signalling. In this study, mechanisms of resistance to imatinib-induced apoptosis in human Meg-01 CML cells were examined. Continuous exposure of cells to step-wise increasing concentrations of imatinib resulted in the selection of 200- and 1000 nM imatinib-resistant sub-lines referred to as Meg-01/IMA-0,2 and Meg-01/1MA-1, respectively. MTT cell proliferation, cell cycle analyses and trypan blue dye exclusion analyses showed that Meg-0l/IMA-1 cells were resistant to imatinib-induced apoptosis as compared to parental sensitive cells. There was an increased expression of BCR/ABL, Bcl-2 and an increase in mitochondrial membrane potential (MMP) detected in resistant cells comparing to parental sensitive cells. There was no mutation detected in imatinib binding site of ABL kinase region. Various diverse mechanisms have been reported for their involvement in the multidrug resistance. In this study, it has been shown that the degree of BCR/ABL expression appears to be directly proportional to the levels of imatinib resistance. In addition, there have been BCR/ABL-independent mechanisms reported for deriving resistance against imatinib. Our results revealed that besides BCR/ABL overexpression, imatinib resistance also depends on the inhibition of apoptosis as a result of up-regulation of anti-apoptotic stimuli and down-regulation of pro-apoptotic stimuli through MMP but does not depend on any mutation on imatinib binding site of ABL kinase.
  • Article
    Citation - WoS: 6
    Citation - Scopus: 7
    Mineral Nutrient Acquisition by Cotton Cultivars Grown Under Salt Stress
    (Taylor and Francis Ltd., 2017) Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yalçın, İbrahim Ertuğrul
    Physiological responses were investigated in two cotton cultivars grown at various concentrations of sodium chloride (NaCl) in order to determine the degree of the tolerance of the cultivars to salt stress and understand the physiological responses with respect to utilization of mineral nutrients. After germination of the seeds of cotton cultivars, they were transferred into standard pots with 210 g sterilized compost and watered with 30 ml Hoagland’s solution containing different concentrations (0, 50, 100, 200, and 400 mM) of NaCl at two-day intervals for 3 months. Growth parameters were measured and the mineral nutrient analyses were done using inductively coupled plasma optical emission spectrometry (ICP-OES, Thermo Fisher Scientific, Waltman, MA). It was observed that plant growth and mineral nutritional status of both cultivars were altered extensively in those grown with NaCl. Excess NaCl reduces the concentrations of certain mineral nutrients and increases that of others, the patterns depending on the mineral nutrient and the plant part and varieties being compared to the control.
  • Article
    Citation - WoS: 625
    Citation - Scopus: 698
    Flow Cytometry: Basic Principles and Applications
    (Taylor and Francis Ltd., 2017) Adan, Aysun; Alizada, Günel; Kiraz, Yağmur; Baran, Yusuf; Nalbant, Ayten
    Flow cytometry is a sophisticated instrument measuring multiple physical characteristics of a single cell such as size and granularity simultaneously as the cell flows in suspension through a measuring device. Its working depends on the light scattering features of the cells under investigation, which may be derived from dyes or monoclonal antibodies targeting either extracellular molecules located on the surface or intracellular molecules inside the cell. This approach makes flow cytometry a powerful tool for detailed analysis of complex populations in a short period of time. This review covers the general principles and selected applications of flow cytometry such as immunophenotyping of peripheral blood cells, analysis of apoptosis and detection of cytokines. Additionally, this report provides a basic understanding of flow cytometry technology essential for all users as well as the methods used to analyze and interpret the data. Moreover, recent progresses in flow cytometry have been discussed in order to give an opinion about the future importance of this technology.
  • Article
    Citation - WoS: 16
    Citation - Scopus: 16
    Screening of Damage Induced by Lead (pb) in Rye (secale Cereale L.) – a Genetic and Physiological Approach
    (Taylor and Francis Ltd., 2016) Özyigit, İbrahim İlker; Doğan, İlhan; İğdelioğlu, Sezen; Filiz, Ertuğrul; Karadeniz, Sedat; Uzunova, Zeynep
    The fields in which lead (Pb) finds application in the modern world have increased dramatically in recent years. As a consequence of this intensive utilization of Pb, its toxicity tends to pose more and more environmental problems. The aim of this study was to evaluate the genotoxic potential of Pb and to characterize some physiological parameters in Secale cereale under Pb stress. Plants were subjected to different exposure levels of Pb (0, 100, 200 and 400 µmol/L) for two weeks. At the end of the experimental period, the effects of Pb exposure on the photosynthetic pigments content (chlorophyll a and b, total chlorophyll, chlorophyll a/b and carotenoids) and genetic material of S. cereale were studied. To evaluate the genotoxic effect of Pb, random amplified polymorphic DNA – polymerase chain reaction (RAPD-PCR) was employed. The obtained results showed alteration in the photosynthetic pigments content and RAPD-PCR profiles of S. cereale grown in the presence of Pb. The alterations in the RAPD-PCR profiles following Pb treatments appeared to be losses of normal bands and occurrences of new bands compared to unexposed plantlets. Overall, the content of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids decreased by 6.68%, 6.08%, 2.89% and 8.57%, respectively, under severe Pb stress (400 µmol/L).
  • Article
    Citation - WoS: 278
    Citation - Scopus: 295
    Molecular Mechanisms of Drug Resistance and Its Reversal in Cancer
    (Taylor and Francis Ltd., 2016) Kartal Yandım, Melis; Adan Gökbulut, Aysun; Baran, Yusuf
    Chemotherapy is the main strategy for the treatment of cancer. However, the main problem limiting the success of chemotherapy is the development of multidrug resistance. The resistance can be intrinsic or acquired. The resistance phenotype is associated with the tumor cells that gain a cross-resistance to a large range of drugs that are structurally and functionally different. Multidrug resistance arises via many unrelated mechanisms, such as overexpression of energy-dependent efflux proteins, decrease in uptake of the agents, increase or alteration in drug targets, modification of cell cycle checkpoints, inactivation of the agents, compartmentalization of the agents, inhibition of apoptosis and aberrant bioactive sphingolipid metabolism. Exact elucidation of resistance mechanisms and molecular and biochemical approaches to overcome multidrug resistance have been a major goal in cancer research. This review comprises the mechanisms guiding multidrug resistance in cancer chemotherapy and also touches on approaches for reversing the resistance.
  • Article
    Citation - WoS: 18
    Citation - Scopus: 20
    Assessment of Cd-Induced Genotoxic Damage in Urtica Pilulifera L. Using Rapd-Pcr Analysis
    (Taylor and Francis Ltd., 2016) Doğan, İlhan; Özyiğit, İbrahim İlker; Tombuloğlu, Güzin; Sakçalı, Mehmet Serdal; Tombuloğlu, Hüseyin
    Plants can be used as biological indicators in assessing the damage done by bioaccumulation of heavy metals and their negative impact on the environment. In the present research, Roman nettle (Urtica pilulifera L.) was employed as a bioindicator for cadmium (Cd) pollution. The comparisons between unexposed and exposed plant samples revealed inhibition of the root growth (∼25.96% and ∼45.92% after treatment with 100 and 200 µmol/L Cd concentrations, respectively), reduction in the total soluble protein quantities (∼53.92% and ∼66.29% after treatment with 100 and 200 µmol/L Cd concentrations, respectively) and a gradual genomic instability when the Cd concentrations were increased. The results indicated that alterations in randomly amplified polymorphic DNA (RAPD) profiles, following the Cd treatments, included normal band losses and emergence of new bands, when compared to the controls. Also, the obtained data from F1 plants, utilized for analysis of genotoxicity, revealed that DNA alterations, occurring in parent plants due to Cd pollution, were transmitted to the next generation.
  • Article
    Citation - WoS: 9
    Citation - Scopus: 10
    A Primer To Molecular Phylogenetic Analysis in Plants
    (Taylor and Francis Ltd., 2015) Uncu, Ayşe Özgür; Uncu, Ali Tevfik; Çelik, İbrahim; Doğanlar, Sami; Frary, Anne
    Reconstructing a tree of life by inferring evolutionary history is an important focus of evolutionary biology. Phylogenetic reconstructions also provide useful information for a range of scientific disciplines such as botany, zoology, phylogeography, archaeology and biological anthropology. Until the development of protein and DNA sequencing techniques in the 1960s and 1970s, phylogenetic reconstructions were based on fossil records and comparative morphological/physiological analyses. Since then, progress in molecular phylogenetics has compensated for some of the shortcomings of phenotype-based comparisons. Comparisons at the molecular level increase the accuracy of phylogenetic inference because there is no environmental influence on DNA/peptide sequences and evaluation of sequence similarity is not subjective. While the number of morphological/physiological characters that are sufficiently conserved for phylogenetic inference is limited, molecular data provide a large number of datapoints and enable comparisons from diverse taxa. Over the last 20 years, developments in molecular phylogenetics have greatly contributed to our understanding of plant evolutionary relationships. Regions in the plant nuclear and organellar genomes that are optimal for phylogenetic inference have been determined and recent advances in DNA sequencing techniques have enabled comparisons at the whole genome level. Sequences from the nuclear and organellar genomes of thousands of plant species are readily available in public databases, enabling researchers without access to molecular biology tools to investigate phylogenetic relationships by sequence comparisons using the appropriate nucleotide substitution models and tree building algorithms. In the present review, the statistical models and algorithms used to reconstruct phylogenetic trees are introduced and advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed.
  • Article
    Citation - WoS: 22
    Citation - Scopus: 25
    Influence of Aluminum on Mineral Nutrient Uptake and Accumulation in Urtica Pilulifera L.
    (Taylor and Francis Ltd., 2014) Doğan, İlhan; Özyiğit, İbrahim İlker; Demir, Göksel
    Pollutants can have detrimental effects on living organisms. They can cause toxicity, damaging cells, tissues and organs because of their high concentrations or activities. Plants provide a useful system for screening and monitoring environmental pollutants. Among pollutants, aluminum is considered as a primary growth limiting factor for plants resulting in decreased plant growth and development. Although considered to be a non-essential and highly toxic metal ion for growth and development, aluminum (Al) is easily absorbed by plants. Urticaceae family members have high nutrient requirements demonstrated by leaves containing high levels of calcium (Ca), iron (Fe), magnesium (Mg), and nitrogen (N). Urtica pilulifera is one of the important traditional medicinal plants in Turkey. In this study, U. pilulifera was used as a bioindicator to investigate the possible differences in the absorption and accumulation of mineral nutrients at different levels of the Al exposure and examine the mineral nutrition composition of U. pilulifera under Al stress. Also, some growth parameters (leaf-stem fresh and dry weights, root dry weights, stem lengths and leaf surface area) were investigated. U. pilulifera seedlings were grown for two months in growth-room conditions and watered with spiked Hoagland solution, which contained 0, 100, and 200 μM aluminium chloride (AlCl3). It was observed that macro- and micro-nutritional status of roots and leaves was altered by Al exposure. The concentrations of some macro- and micronutrients were reduced while concentrations of others were increased by excess of Al. Some macro- and micronutrients were increased at low level of Al whereas reductions were observed at high level of Al, and vice versa. The patterns were dependent on the macro- or micronutrient and the plant part.
  • Article
    Citation - WoS: 7
    Citation - Scopus: 10
    Biotechnology for Enhanced Nutritional Quality in Plants
    (Taylor and Francis Ltd., 2013) Uncu, Ayşe Özgür; Doğanlar, Sami; Frary, Anne
    With almost 870 million people estimated to suffer from chronic hunger worldwide, undernourishment represents a major problem that severely affects people in developing countries. In addition to undernourishment, micronutrient deficiency alone can be a cause of serious illness and death. Large portions of the world population rely on a single, starch-rich crop as their primary energy source and these staple crops are generally not rich sources of micronutrients. As a result, physical and mental health problems related to micronutrient deficiencies are estimated to affect around two billion people worldwide. The situation is expected to get worse in parallel with the expanding world population. Improving the nutritional quality of staple crops seems to be an effective and straightforward solution to the problem. Conventional breeding has long been employed for this purpose but success has been limited to the existing diversity in the gene pool. However, biotechnology enables addition or improvement of any nutrient, even those that are scarce or totally absent in a crop species. In addition, biotechnology introduces speed to the biofortification process compared to conventional breeding. Genetic engineering was successfully employed to improve a wide variety of nutritional traits over the last decade. In the present review, progress toward engineering various types of major and minor constituents for the improvement of plant nutritional quality is discussed. © 2013 Copyright Taylor and Francis Group, LLC.
  • Article
    Citation - WoS: 57
    Citation - Scopus: 67
    Resveratrol and Quercetin-Induced Apoptosis of Human 232b4 Chronic Lymphocytic Leukemia Cells by Activation of Caspase-3 and Cell Cycle Arrest
    (Taylor and Francis Ltd., 2013) Adan Gökbulut, Aysun; Apohan, Elif; Baran, Yusuf
    Chronic lymphocytic leukemia (CLL), defined by accumulation of pathogenic B cells, has a very complex biology due to various factors such as inherited, host, and enviromental factors. Recently, finding new therapeutic agents or development of novel treatment strategies have been paid attention. Resveratrol and quercetin, important phytoalexins found in many plants, have been reported to have cytotoxic effects on various types of cancer. In this study, we examined cytotoxic, cytostatic, and apoptotic effects of these two important phenolic compounds on 232B4 human CLL cells. Cytotoxic effects of resveratrol and quercetin were determined by MTT cell proliferation assay. Changes in caspase-3 enzyme activity were measured using caspase-3 colorimetric assay. Annexin V-FITC/PI double staining was performed to measure apoptotic cell population. Effects of resveratrol and quercetin on cell cycle profiles of CLL cells were investigated by flow cytometry. Treatment of CLL cells with resveratrol and quercetin caused dose dependent inhibition of cell proliferation and increased apoptotic cell population through induction of caspase-3 activity. Cell cycle analysis displayed cell cycle arrest mainly in G0/G1 for both polyphenols. Our data, in total, showed for the first time that resveratrol and quercetin might block CLL growth through inducing apoptosis and cell cycle arrest.