Yazar "Uras, Mehmet Emin" seçeneğine göre listele

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    Abiotic stress-induced regulation of antioxidant genes in different Arabidopsis ecotypes: microarray data evaluation
    (Taylor & Francis Ltd, 2019) Filiz, Ertuğrul; Özyiğit, İbrahim İlker; Saraçoğlu, İbrahim Adnan; Uras, Mehmet Emin; Şen, Uğur; Yalçın, Bahattin
    Although stresses induce generation of reactive oxygen species (ROS), which are highly reactive and toxic, and cause severe damage to cellular components; plants have very efficient enzymatic ROS-scavenging mechanisms. Despite the substantial knowledge produced about these enzymes, we still have limited knowledge regarding their expression patterns in relation to the stress type, duration and strength. Thus, taking advantage of microarray data, this work evaluated the abiotic stresses (salt, cold, heat and light) induced regulation of six antioxidant enzymes, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione peroxidase (GPX), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR), in 10 natural Arabidopsis ecotypes. The expression profiles of 36 genes encoding six enzymatic antioxidants including CSD1-3, FSD1-3, MSD1-2, CAT1-3, APX1-6, APXT, APXS, GPX1-8, MDAR1-5 and DHAR1-4 were investigated. In particular, FSD1, FSD2, CSD1 and CSD2 genes coding for SOD; CAT2 and CAT3 for CAT; APX3-6, APXT and APXS for APX; GPX1, GPX2, GPX5, GPX6 and GPX7 for GPX; MDAR2-4 for MDHAR; and DHAR1 and DHAR3 for DHAR families appeared to be more differentially expressed under given stress conditions. Primarily, high light as well as salt and cold stresses considerably up-regulated the gene expression, whereas cold stress significantly led to the down-regulation of genes. The overall expression pattern of ecotypes suggested that the studied Arabidopsis genotypes had different stress tolerance.
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    GENETIC DIVERSITY AND PHYLOGENETIC ANALYSES OF TURKISH RICE VARIETIES REVEALED BY ISSR MARKERS AND CHLOROPLAST trnL-F REGION
    (Parlar Scientific Publications (P S P), 2018) Filiz, Ertuğrul; Uras, Mehmet Emin; Özyiğit, İbrahim İlker; Şen, Uğur; Güngör, Hüseyin
    A set of 17 Turkish rice (Oryza sativa L.) varieties (TRVs) were characterized using inter simple sequence repeat (ISSR) markers to study genetic diversity. Also, the sequences of trnL((UAA))-F-(GAA) intergenic spacer (IGS) regions were used to evaluate the phylogenetic relationships of TRVs. According to ISSR data, the observed number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (h), Shannon's information index (I), and overall polymorphism were found as 1.62, 1.38, 0.22, 0.32, and 61.7%, respectively. The genetic distance values were identified between 1.732and 4.583, and replicon size varied from 200 bp to 1600 bp. The ISSR-UPGMA (unweighted pair group method with arithmetic mean) similarity tree and PCA (principal component analysis) exhibited different cluster topologies based on pedigree. All trnL-F regions were found as 306 bp in length, and GC content was found between 34.31% and 34.97%. The nucleotide diversities were found as pi: 0.00954 and theta: 0.03595, while Tajima's D was found as -0.382. The phylogenetic analyses revealed that trnL-F sequences are effective molecular tools in resolving phylogenetic relationships. Consequently, our findings could be useful in planning future Turkish rice breeding strategies for general rice germplasm improvement.
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    Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequences
    (Czech Academy Agricultural Sciences, 2024) Uras, Mehmet Emin; Filiz, Ertugrul; Sen, Ugur; Ozyigit, Ibrahim Ilker
    Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovasi District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures.
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    Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.)
    (Springer, 2016) Vatansever, Recep; Koç, İbrahim; Özyiğit, İbrahim İlker; Şen, Uğur; Uras, Mehmet Emin; Anjum, Naser A.; Filiz, Ertuğrul
    Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts. StSULTR genes were mapped on seven S. tuberosum chromosomes. Annotation of StSULTR genes was also done as StSULTR I-IV at group level based mainly on the phylogenetic distribution with Arabidopsis SULTRs. Several tandem and segmental duplications were identified between StSULTR genes. Among these duplications, Ka/Ks ratios indicated neutral nature of mutations that might not be causing any selection. Two segmental and one-tandem duplications were calculated to occur around 147.69, 180.80 and 191.00 million years ago (MYA), approximately corresponding to the time of monocot/dicot divergence. Two other segmental duplications were found to occur around 61.23 and 67.83 MYA, which is very close to the origination of monocotyledons. Most cis-regulatory elements in StSULTRs were found associated with major hormones (such as abscisic acid and methyl jasmonate), and defense and stress responsiveness. The cis-element distribution in duplicated gene pairs indicated the contribution of duplication events in conferring the neofunctionalization/s in StSULTR genes. Notably, RNAseq data analyses unveiled expression profiles of StSULTR genes under different stress conditions. In particular, expression profiles of StSULTR III members suggested their involvement in plant stress responses. Additionally, gene co-expression networks of these group members included various regulatory factors, stress and signaling proteins, and housekeeping and some other proteins with unknown functions.
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    Genome-wide identification and expression profiling of EIL gene family in woody plant representative poplar (Populus trichocarpa)
    (Elsevier Science Inc, 2017) Filiz, Ertuğrul; Vatansever, Recep; Özyiğit, İbrahim İlker; Uras, Mehmet Emin; Şen, Uğur; Anjum, Naser A.; Pereira, Eduarda
    This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chrl, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80 280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (similar to 80-280 residues including EIN3 domain) was substantially conserved. The second half (-300-600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, praline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3-and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules. (C) 2017 Elsevier Inc. All rights reserved.
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    Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis
    (Taylor & Francis Inc, 2017) Vatansever, Recep; Uras, Mehmet Emin; Şen, Uğur; Özyiğit, İbrahim İlker; Filiz, Ertuğrul
    A transcription factor DREB1A (dehydration-responsive element-binding 1A) gene was amplified and sequenced from the common bean (Phaseolus vulgaris). PvDREB1A had a 777 base pairs (bp) open reading frame encoding a protein of 225 residues. The protein sequence contained a conserved DNA-binding AP2 domain of about 60 residues and a nuclear localization signal (NLS) at N-terminus site. PvDREB1A demonstrated high homology with other DREB1 members only in AP2 domain and NLS site. The phylogenetic distribution of different DREB members showed three main groups as DREB1-3 and PvDREB1A was a member of DREB1 group. Homology modeling and secondary structure analyses revealed that PvDREB1A AP2 domain was packed into the three-stranded antiparallel beta sheets (beta 1-3) and an alpha helix (alpha 1) almost parallel to these beta sheets. Moreover, DNA-binding AP2 domain of PvDREB1A and GCC-box containing double helix DNA were docked. The docking analysis showed that PvDREB1A AP2 domain could bind to the major groove of the DNA by three-stranded antiparallel beta sheets, with residues Gly86 or Thr87 in beta 1-sheet and Arg63 or Arg64 in beta 3-sheet. The docked complex also indicated that AP2 domain has a preferential for the binding of GCC stretches in the double helix DNA. A total of 36 reliably estimated hot spots residues were identified with high mutability grade but none of these residues was essential for the protein function since they are located at outside the DNA-binding AP2 domain of PvDREB1A.