Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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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 Citation - WoS: 6Citation - Scopus: 3Determining Element Accumulations in Turkish Red Pine Used as a Bioindicator for Estimating of Existing Pollution on Both Sides of Bosphorus in İstanbul(Parlar Scientific Publications, 2020) Yalçın, İbrahim Ertuğrul; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yarcı, CelalEvergreen Turkish red pine tree shows wide distribution around Aegean and Mediterranean regions in Turkey. Herein work investigated the mineral nutrient status of Turkish red pine as a bioindicator for revealing the impact of existing pollution on both sides of Bosphorus in Istanbul. For this, Al, B, Ca, Cu, Fe, K, Mg, Na and Zn concentrations were determined in unwashed and washed leaves and barks of the plant and soil samples. The standard procedures were applied and the determinations of element concentrations in all samples were done using ICP-OES. The sample collections were performed at five different locations in Istanbul, 4 from the Bosphorus region and one from Prince Island (as control). The highest element concentrations (in mg kg(-1) DW) in plant parts were recorded between 109.10 +/- 1.68 and 120.58 +/- 1.75 for Al, 10.18 +/- 0.14 and 12.52 +/- 0.17 for B, 8765.42 +/- 92.41 and 9600.69 +/- 102.22 for Ca, 10.91 +/- 0.13 and 11.73 +/- 0.16 for Cu, 226.85 +/- 3.01 and 254.07 +/- 3.20 for Fe, 4050.69 +/- 48.51 and 4477.08 +/- 52.34 for K, 794.58 +/- 9.82 and 878.33 +/- 10.07 for Mg, 1255.14 +/- 14.67 and 1374.31 +/- 18.55 for Na and 34.92 +/- 0.49 and 37.25 +/- 0.57 for Zn while the highest element concentrations (in mg kg(-1) DW) in co-located soil samples were measured between 5470.42 +/- 66.48 and 6046.25 +/- 73.54 for Al, 14.86 +/- 0.20 and 16.43 +/- 0.29 for B, 4600.56 +/- 55.22 and 4984.86 +/- 62.71 for Ca, 22.33 +/- 0.36 and 25.07 +/- 0.48 for Cu, 5500.01 +/- 71.05 and 5953.06 +/- 80.16 for Fe, 1819.44 +/- 23.51 and 2029.17 +/- 27.04 for K, 4108.75 +/- 50.77 and 4714.17 +/- 58.09 for Mg, 111.11 +/- 1.82 and 122.08 +/- 2.45 for Na and 117.10 +/- 2.33 and 126.86 +/- 2.61 for Zn.Article Citation - WoS: 6Citation - Scopus: 9Detection of Physiological and Genotoxic Damages Reflecting Toxicity in Kalanchoe Clones(Global Network Environmental Science & Technology, 2016) Özyiğit, İbrahim İlker; Yılmaz, S.; Doğan, İlhan; Sakçalı, Mehmet Serdal; Tombuloğlu, Güzin; Demir, GökselIn order to make assessments in understanding of physiological and genotoxic effects of imposing cadmium (Cd) on photosynthetic pigment contents along with the changes occurring in genetic material of Kalanchoe plants were used in relation to various Cd-treatments. Young plantlets were originated from a single host plant as clones, and developed in vitro. Developed clones were grown in standard pots with daily watering of Hoagland solution (20 ml) containing different concentrations of cadmium chloride for two months. Cd concentrations of the collected samples were measured by employing ICP-OES and RAPD-PCR technique was applied for detecting the genotoxic effects of Cd. After two month of experimental period, the comparisons between unexposed and exposed Kalanchoe clone groups revealed reductions in photosynthetic pigment contents, especially at the highest level of Cd exposure and a genomic instability when application of Cd concentration increases. RAPD-PCR analyses demonstrated the distinguishable banding pattern in number and band intensities between Cd-treated and control groups. In addition, progressive Cd accumulations in leaves, stems and roots of plant samples were observed when the application of exposure level increased.Article Evaluation of Aluminum Stress Induced Antibacterial and Antifungal Activities in Roman Nettle(Parlar Scientific Publications, 2019) Özyiğit, İbrahim İlker; Doğan, İlhan; Yalçın, İbrahim Ertuğrul; Severoğlu, ZekiIn this current work, Roman nettle (Urtica pilulifera L.), a traditional medicinal plant that is very common and widespread species throughout Asia, Europe, and Northern Africa, was used as a model plant to investigate changes in antimicrobial activity following the application of aluminum stress. U pilulifera seedlings were grown in growth-room conditions and 0, 100, and 200 M AlCl3 were applied to the plants together with Hoagland solution (20 ml) for two months. The antimicrobial activities were tested against nine strains of bacteria (Salmonella sp., Staphyllococcus aureus, Escherichia coli, E. coli O157:H7 and Bacillus cereus) and fungus (Penicillum sp., Saccharomyces cerevisiae, Candida tropicans and C. albicans) by using the disc diffusion and agar well methods. The accumulated Al was measured by using ICP-OES in the leaves of studied plant samples. Additionally, a control group (water + 11.31 mg l(-1) Al) was prepared and applied to selected bacteria and fungi in order to understand the reason for obtained antimicrobial activities of Roman nettle is whether because of the compounds isolated from nettle leaves exposed to Al stress, or Al itself accumulated in leaves. The data proved that inhibitory antimicrobial effects were altered in U pilulifera upon the application of Al stress, especially on fungi species.Article Citation - WoS: 3Ecophysiological Properties of Turkish Endemic Centaurea Consanguinea Dc.(Parlar Scientific Publications, 2019) Eskin, Bülent; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yarcı, Celal; Serin, MemduhThis physiological and ecological study was performed on Centaurea consanguinea DC. to acquire information about certain characteristics (bioclimatic, edaphic, topographic, biotic etc.) of its habitat and distribution in Turkey, determine the requirements for germination, explore the soil-plant relations and obtain data on certain aspects of its population biology. Plant and co-located soil samples were collected from Amasya and Havza District (Samsun) in Turkey using standard methods. Various analyzes were employed for determining of physical, chemical and biological properties of the plant species and its co-located soils including pH, total protein and electrical conductivity (EC), soil texture, contents of mineral nutrition and other physical and chemical parameters and the results were presented. Nutrient amounts (in %) were found to be in the ranges of 0.01-0.007 for N, 0.0008-0.001 for P, 0.01-0.09 for K, 0.0002-0.0003 for Na in the soils and 2.25 for N, 0.0068 for P, 0.07 for K and 0.02 for Na in the plant, respectively. Also, it was observed that germination ratios of the seeds were depended on various factors.Book Part Citation - WoS: 10Citation - Scopus: 16Plant-Microbe Interactions in Phytoremediation(Elsevier Ltd., 2014) Özyiğit, İbrahim İlker; Doğan, İlhanOur atmosphere, water resources and soil are becoming increasingly contaminated with inorganic and organic compounds as a result of anthropogenic-driven inputs, mainly from industry, mining, motorized traffic, agriculture, logging and military actions. Alleviation and prevention of environmental pollution can be achieved by utilization of plants and their associated microbes. Recent advances in plant-microbe interaction research revealed that plants are able to shape their rhizosphere microbiome through active secretion of substrates that are known to vary between plant species. Soil-borne microorganisms such as actinobacteria, algae, protozoa and different types of bacteria having different capabilities of functional activities can vary extensively in soils and occur in associations in the rhizosphere of plants. Microbial associations are known to affect mobility and availability of substances to the plant through the release of chelating agents, acidification, phosphate solubilization and redox changes and exudates derived from the plant can help to stimulate the survival and action of these microorganisms. A broad knowledge about the mechanisms in plants for the uptake, translocation, storage, and detoxification of contaminants, and interactions between plants and microorganisms are critical in developing technologies and best management practices for environmental clean-up. A comprehensive understanding of interactions between plants and rhizospheric microorganisms in the rhizosphere and plant-based processes will provide new opportunities to develop more efficient plants and better management practices for removal of contaminants. This chapter reviews plant-microbe interactions in phytoremediation with particular reference to the microbial dynamics in the rhizosphere of plants growing on contaminated soils.Article Citation - WoS: 6Citation - Scopus: 7Mineral Nutrient Acquisition by Cotton Cultivars Grown Under Salt Stress(Taylor and Francis Ltd., 2017) Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yalçın, İbrahim ErtuğrulPhysiological 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: 16Citation - Scopus: 16Screening 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, ZeynepThe 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: 2Citation - Scopus: 2Analysis of Est-Ssrs in Silver Birch (betula Pendula Roth.)(Northeast Forestry University, 2016) Filiz, Ertuğrul; Doğan, İlhan; Özyigit, İbrahim İlkerSimple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs (expressed sequence tags) of Betula pendula (silver birch) were analyzed for in silico mining of EST-SSRs, protein annotation, open reading frames (ORFs), designing primers, and identifying codon repetitions. In B. pendula, the frequency of ESTs containing SSRs was 7.8 % with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and di-nucleotide SSR motifs (65.9 %) were found to be the most abundant type of repeat motif followed by tri- (27.1 %), tetra- (4.8 %), and penta- (2.2 %) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 5′ UTR (58.43 %), followed by in ORF (31.46 %) and in 3′ UTR (8.43 %). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein, and transferase protein. For a total of 102 SSRs (57.3 %) with significant matches, a set of 102 primers (100 %) with forward and reverse strands was designed by using Primer3 software. Serine (Ser, 19.6 %) was predominant in putative encoded amino acids and most of amino acids showed nonpolar (35.3 %) nature. Our data provide resources for B. pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.