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: 3Citation - Scopus: 5A Novel Thermophilic Hemoprotein Scaffold for Rational Design of Biocatalysts(Springer Verlag, 2018) Efua Aggrey Fynn, Joana; Sürmeli, Nur BaşakHemoproteins are commonly found in nature, and involved in many important cellular processes such as oxygen transport, electron transfer, and catalysis. Rational design of hemoproteins can not only inspire novel biocatalysts but will also lead to a better understanding of structure-function relationships in native hemoproteins. Here, the heme nitric oxide/oxygen-binding protein from Caldanaerobacter subterraneus subsp. tengcongensis (TtH-NOX) is used as a novel scaffold for oxidation biocatalyst design. We show that signaling protein TtH-NOX can be reengineered to catalyze H2O2 decomposition and oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) by H2O2. In addition, the role of the distal tyrosine (Tyr140) in catalysis is investigated. The mutation of Tyr140 to alanine hinders the catalysis of the oxidation reactions. On the other hand, the mutation of Tyr140 to histidine, which is commonly observed in peroxidases, leads to a significant increase of the catalytic activity. Taken together, these results show that, while the distal histidine plays an important role in hemoprotein reactions with H2O2, it is not always essential for oxidation activity. We show that TtH-NOX protein can be used as an alternative scaffold for the design of novel biocatalysts with desired reactivity or functionality. H-NOX proteins are homologous to the nitric oxide sensor soluble guanylate cyclase. Here, we show that the gas sensor protein TtH-NOX shows limited capacity for catalysis of redox reactions and it can be used as a novel scaffold in biocatalysis design. [GRAPHICS] .Article Citation - WoS: 12Citation - Scopus: 18Synergistic Antimicrobial Effects of Activated Lactoferrin and Rosemary Extract in Vitro and Potential Application in Meat Storage(Springer Verlag, 2020) Soyer, Ferda; Keman, Deniz; Eroğlu, Erdal; Türe, HasanThis study aimed to explore the antimicrobial effects of activated lactoferrin (ALF) and rosemary extract (RE) on Escherichia coli O157:H7, Salmonella Enteritidis and Listeria monocytogenes, and to investigate their application potential in the meat storage. Minimum inhibitory concentrations (MICs) of ALF, RE and ALF-RE combinations were determined via microtiter plate assay. MICs of ALF were 1% for E. coli O157:H7; 0.5% for S. Enteritidis and 0.1% for L. monocytogenes. While 15% RE inhibited L. monocytogenes; 30% RE partially inhibited E. coli O157:H7 and S. Enteritidis growth. Synergistic effect of ALF and RE on the inhibition of E. coli O157:H7 increased the activity of ALF two to three folds. Food application of antimicrobials was performed by dipping of meat samples. Both ALF and RE were found effective in the prevention of L. monocytogenes growth about two logs. According to the data, choice of natural antimicrobials may be promising in food preservation.Article Citation - WoS: 18Citation - Scopus: 29Cry1ac-Mediated Resistance To Tomato Leaf Miner (tuta Absoluta) in Tomato(Springer Verlag, 2017) Şelale, Hatice; Dağlı, Fatih; Mutlu, Nedim; Doğanlar, Sami; Frary, AnneTomato leaf miner (Tuta absoluta) is a major pest of tomato in regions with hot climates such as South America and the Mediterranean. This insect feeds on almost every part of the plant and forms galleries while feeding on the plant’s inner tissues. Thus, it can cause plant death and is costly and difficult to control with chemical sprays. In this study, we transferred a modified Bacillus thuringiensis cry1Ac gene to tomato plants via Agrobacterium tumefaciens mediated transformation. Introduction of the cry1Ac gene to the tomato genome was confirmed with PCR and Southern blot analysis in 12 independent events. Insertion sites of the transgene in the tomato genome were determined with TAIL-PCR (thermal asymmetric interlaced polymerase chain reaction) for four selected transgenic lines. Cry1Ac gene expression was verified at both the transcriptional and translational levels, with RT-qPCR and Western blot analyses, respectively. Expression of the Cry1Ac protein in tomato resulted in T. absoluta mortality rates of 38–100% depending on transgenic line. In addition, gallery formation was reduced in 57–100% of the transgenic plants. Moreover, it was found that a single copy of the gene in the hemizygous condition is sufficient to confer tolerance to leaf miner. This is the first reported development of tomato plants resistant to T. absoluta. These transgenic plants are promising for development of commercial tomato cultivars resistant to leaf miner, which will limit the use of environmentally harmful chemicals for control of this pest.Article Citation - WoS: 17Citation - Scopus: 20Molecular Genetic Diversity of the Turkish National Hazelnut Collection and Selection of a Core Set(Springer Verlag, 2017) Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Duyar, Ömür; Doğanlar, Sami; Frary, AnneEuropean hazelnut (Corylus avellana L.) is an economically and nutritionally important nut crop with wild and cultivated populations found throughout Europe and in parts of Asia. This study examined the molecular genetic diversity and population structure of 402 genotypes including 143 wild individuals, 239 landraces, and 20 cultivars from the Turkish national hazelnut collection using simple sequence repeat (SSR) markers. A total of 30 SSR markers yielded 407 polymorphic fragments. Diversity analysis of the Turkish hazelnut genotypes indicated that they fell into three subpopulations according to ad hoc statistics and neighbor-joining algorithm. Although all cultivars clustered together, they overlapped with the wild accessions and landraces. Thus, the dendrogram, principal coordinate, and population structure analyses suggest that they share the same gene pool. A total of 78 accessions were selected as a core set to encompass the molecular genetic and morphological diversity present in the national collection. This core set should have priority in preservation efforts and in trait characterization.Article Citation - WoS: 30Citation - Scopus: 36Molecular Genetic Diversity and Association Mapping of Nut and Kernel Traits in Slovenian Hazelnut (corylus Avellana) Germplasm(Springer Verlag, 2017) Öztürk, Süleyman Can; Öztürk, Saniye Elvan; Çelik, İbrahim; Stampar, Franci; Veberic, Robert; Doğanlar, Sami; Solar, Anita; Frary, AnneEuropean hazelnut (Corylus avellana L.), cultivated in several areas of the world including Europe, Anatolia, and the USA, is an economically important nut crop due to its high mineral, oleic acid, amino acid, and phenolic compound content and pleasant flavor. This study examined molecular genetic diversity and population structure of 54 wild accessions and 48 cultivars from the Slovenian national hazelnut collection using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Eleven AFLP primer combinations and 49 SSR markers yielded 532 and 504 polymorphic fragments, respectively. As expected for a wind-pollinated, self-incompatible species, levels of genetic diversity were high with cultivars and wild accessions having mean dissimilarity values of 0.50 and 0.60, respectively. In general, cultivars and wild accessions clustered separately in dendrogram, principal coordinate, and population structure analyses with regional clustering of the wild material. The accessions were also characterized for ten nut and seven kernel traits and some wild accessions were shown to have breeding potential. Morphological principal component analysis showed distinct clustering of cultivars and wild accessions. An association mapping panel composed of 64 hazelnut cultivars and wild accessions had considerable variation for the nut and kernel quality traits. Morphological and molecular data were associated to identify markers controlling the traits. In all, 49 SSR markers were significantly associated with nut and kernel traits [P < 0.0001 and LD value (r2) = 0.15–0.50]. This work is the first use of association mapping in hazelnut and has identified molecular markers associated with important quality parameters in this important nut crop.Article Citation - WoS: 15Citation - Scopus: 18Molecular Diversity and Identification of Alleles for Verticillium Wilt Resistance in Elite Cotton (gossypium Hirsutum L.) Germplasm(Springer Verlag, 2017) Akköse Baytar, Asena; Erdoğan, Oktay; Frary, Anne; Frary, Amy; Doğanlar, SamiCotton is an important crop in the textile, food and pharmaceutical industries. In the present study, a panel of 108 elite cotton (Gossypium hirsutum L.) lines was genotyped with 177 genome-wide SSR markers to assess genetic diversity, linkage disequilibrium, population structure and association analyses. A total of 967 loci were assayed and the lines fell into four main groups with a mean genetic distance of 39%. The linkage disequilibrium (LD) decay rate was estimated to be 20–30 cm (r2 ≤ 0.5). Association analyses were performed with both general linear model and mixed linear model methods to identify SSR marker loci linked to Verticillium wilt resistance. Verticillium wilt is a fungal disease that causes huge yield losses in cotton production throughout the world. A total of 26 marker loci distributed on 14 chromosomes were associated with resistance at p ≤ 0.05. Eight of the 26 associated marker loci were highly significant (p < 0.01). The phenotypic variation explained (r2) by individual markers ranged from 3.2% to 8.2%. Three of the 26 marker loci (JESPR153, JESPR274 and CIR218) were consistent with previous studies. Our results should be useful in improving Verticillium wilt resistance in cotton breeding lines.Article Citation - WoS: 13Citation - Scopus: 22Development of a Snp-Based Caps Assay for the Me1 Gene Conferring Resistance To Root Knot Nematode in Pepper(Springer Verlag, 2015) Uncu, Ali Tevfik; Çelik, İbrahim; Devran, Zübeyir; Frary, Anne; Frary, Amy; Doğanlar, SamiRoot knot nematodes (Meloidogyne spp.) are significant agricultural pests on many crops, including pepper (Capsicum annuum). Host plant resistance offers the most sustainable means of controlling this pest. A cluster of genes on chromosome 9 confers resistance, with Me1 providing protection against three nematode species: M. incognita, M. javanica and M. arenaria. We describe the development of a codominant CAPS marker located 1.13 cM away from the Me1 gene. This marker should be useful for marker assisted selection of nematode resistance in pepper breeding programs.Article Citation - WoS: 18Citation - Scopus: 18High Resolution Map of Eggplant (solanum Melongena) Reveals Extensive Chromosome Rearrangement in Domesticated Members of the Solanaceae(Springer Verlag, 2014) Doğanlar, Sami; Frary, Amy; Daunay, Marie Christine; Huvenaars, Koen H J; Mank, Rolf A.; Frary, AnneA linkage map of eggplant was constructed for an interspecific F2 population derived from a cross between Solanum linnaeanum MM195 and S. melongena MM738. The map contains 400 AFLP® (amplified fragment length polymorphism), 348 RFLP (restriction fragment length polymorphism) and 116 COSII (conserved ortholog set) markers. The 864 mapped markers encompass 12 linkage groups, span 1,518 cM and are spaced at an average interval of 1.8 cM. Use of orthologous markers allowed confirmation of the established syntenic relationships between eggplant and tomato chromosomes and helped delineate the nature of the 33 chromosomal rearrangements and 11 transpositions distinguishing the two species. This genetic map provides a 2- to 3-fold improvement in marker density compared to previously published interspecific maps. Because the interspecific mapping population is rich in morphological variation, this greater genome saturation will be useful for QTL (quantitative trait locus) analyses. The recent release of the tomato genome sequence will provide additional opportunities for exploiting this map for comparative genomics and crop improvement.Article Citation - WoS: 54Citation - Scopus: 61Qtl Hotspots in Eggplant (solanum Melongena) Detected With a High Resolution Map and Cim Analysis(Springer Verlag, 2014) Frary, Amy; Frary, Anne; Daunay, Marie Christine; Huvenaars, Koen; Mank, Rolf; Doğanlar, SamiFifty-eight F2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P ≤ 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make it easier to target particular loci for map-based cloning and marker-assisted selection studies.Article Citation - WoS: 33Citation - Scopus: 37Apoptotic Effects of Quercitrin on Dld-1 Colon Cancer Cell Line(Springer Verlag, 2014) Çinçin, Zeynep Birsu; Ünlü, Miray; Kıran, Bayram; Bireller, Elif Sinem; Baran, Yusuf; Çakmakoğlu, BediaQuercetin, which is the most abundant bioflavonoid compound, is mainly present in the glycoside form of quercitrin. Although different studies indicated that quercitrin is a potent antioxidant, the action of this compound is not well understood. In this study, we investigated whether quercitrin has apoptotic and antiproliferative effects in DLD-1 colon cancer cell lines. Time and dose dependent antiproliferative and apoptotic effects of quercitrin were subsequently determined by WST-1 cell proliferation assay, lactate dehydrogenase (LDH) cytotoxicity assay, detection of nucleosome enrichment factor, changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP) and also the localization of phosphatidylserine (PS) in the plasma membrane. There were significant increases in caspase-3 activity, loss of MMP, and increases in the apoptotic cell population in response to quercitrin in DLD-1 colon cancer cells in a time- and dose-dependent manner. These results revealed that quercitrin has antiproliferative and apoptotic effects on colon cancer cells. Quercitrin activity supported with in vivo analyses could be a biomarker candicate for early colorectal carcinoma.