Browsing by Author "Ulu F."

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Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon
(2023-03-01) İncili Ç.Y.; Arslan B.; Çelik E.N.Y.; Ulu F.; Horuz E.; Baloglu M.C.; Çağlıyan E.; Burcu G.; Bayarslan A.U.; Altunoglu Y.C.
Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the cell wall, breaks down the non-covalent bonds between cell wall polysaccharides, causing pressure-dependent cell expansion. Comparative bioinformatics and molecular characterization analysis of the expansin protein family were carried out in the watermelon (Citrullus lanatus) and melon (Cucumis melo) plants in the study. Gene expression levels of expansin family members were analyzed in leaf and root tissues of watermelon and melon under ABA, drought, heat, cold, and salt stress conditions by quantitative real-time PCR analysis. After comprehensive searches, 40 expansin proteins (22 ClaEXPA, 14 ClaEXPLA, and 4 ClaEXPB) in watermelon and 43 expansin proteins (19 CmEXPA, 15 CmEXPLA, 3 CmEXPB, and 6 CmEXPLB) in melon were identified. The greatest orthologous genes were identified with soybean expansin genes for watermelon and melon. However, the latest divergence time between orthologous genes was determined with poplar expansin genes for watermelon and melon expansin genes. ClaEXPA-04, ClaEXPA-09, ClaEXPB-01, ClaEXPB-03, and ClaEXPLA-13 genes in watermelon and CmEXPA-12, CmEXPA-10, and CmEXPLA-01 genes in melon can be involved in tissue development and abiotic stress response of the plant. The current study combining bioinformatics and experimental analysis can provide a detailed characterization of the expansin superfamily which has roles in growth and reaction to the stress of the plant. The study ensures detailed data for future studies examining gene functions including the roles in plant growth and stress conditions.
Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses
(2021-12-01) Arslan B.; İncili Ç.Y.; Ulu F.; Horuz E.; Bayarslan A.U.; Öçal M.; Kalyoncuoğlu E.; Baloglu M.C.; Altunoglu Y.C.
Zucchini and cucumber belong to the Cucurbitaceae family, a group of economical and nutritious food plants that is consumed worldwide. Expansin superfamily proteins are generally localized in the cell wall of plants and are known to possess an effect on cell wall modification by causing the expansion of this region. Although the whole genome sequences of cucumber and zucchini plants have been resolved, the determination and characterization of expansin superfamily members in these plants using whole genomic data have not been implemented yet. In the current study, a genome-wide analysis of zucchini (Cucurbita pepo) and cucumber (Cucumis sativus) genomes was performed to determine the expansin superfamily genes. In total, 49 and 41 expansin genes were identified in zucchini and cucumber genomes, respectively. All expansin superfamily members were subjected to further bioinformatics analysis including gene and protein structure, ontology of the proteins, phylogenetic relations and conserved motifs, orthologous relations with other plants, targeting miRNAs of those genes and in silico gene expression profiles. In addition, various abiotic stress responses of zucchini and cucumber expansin genes were examined to determine their roles in stress tolerance. CsEXPB-04 and CsEXPA-11 from cucumber and CpEXPA-20 and CpEXPLA-14 from zucchini can be candidate genes for abiotic stress response and tolerance in addition to their roles in the normal developmental processes, which are supported by the gene expression analysis. This work can provide new perspectives for the roles of expansin superfamily genes and offers comprehensive knowledge for future studies investigating the modes of action of expansin proteins.
Comparative identification and evolutionary relationship of fatty acid desaturase (FAD) genes in some oil crops: the sunflower model for evaluation of gene expression pattern under drought stress
(2018-07-04) Celik Altunoglu Y.; Unel N.M.; Baloglu M.C.; Ulu F.; Can T.H.; Cetinkaya R.
Sunflower (Helianthus annuus L.) and some oil crops have considerable economic value, making them important for commercial use. The fatty acid content of their seeds is crucial for proper nutrition. Additionally, the desaturation reaction via fatty acid desaturases (FADs) leads to formation of double bonds in fatty acids and is an essential step in fatty acid biosynthesis. This study aimed to identify and compare some fatty acid desaturase gene members in sunflower and other oil crops. Totally, 33 FAD genes from sunflower, 19 from sesame, 20 from canola, 25 from cacao and 46 from flax were analysed. The FAD members had roles in oxidation–reduction processes, fatty acid biosynthetic processes or lipid metabolic processes. Comparative phylogenetic and motif analysis revealed a conserved structure among FAD members belonging to various oil crops. The average Ka/Ks rates calculated on the basis of orthologous gene analysis were 0.04, 0.05 and 0.05 between sunflower and, respectively, canola, cacao and sesame. The most recent divergence time between sunflower and cacao was estimated at an average of 100 million years ago (MYA). This was followed by flax, sesame and canola with an average of 101 MYA, 114 MYA and 149 MYA, respectively. Alpha-helices were dominant in the predicted 3D structures of FAD proteins. The FAB2 expression levels from a drought tolerant sunflower variety were not affected by drought. The characterisation of desaturase family members in economically valuable oil crops could be useful for functional cloning studies to enhance the unsaturated fatty acid contents of the plants.
Dose-dependent functions of fibroblast growth factor 9 regulate the fate of murine XY primordial germ cells
(2017-01-01) Ulu F.; Kim S.; Yokoyama T.; Yamazaki Y.
Male differentiation of primordial germ cells (PGCs) is initiated by the inhibition of entry into meiosis and exposure to male-inducing factor(s), which are regulated by somatic elements of the developing gonad. Fibroblast growth factor 9 (FGF9) produced by pre-Sertoli cells is essential for male gonadal differentiation and also contributes to survival and male differentiation of XY PGCs. However, it is not clear how FGF9 regulates PGC fate. Using a PGC culture system, we identified dose-dependent, fate-determining functions of FGF9 in XY PGCs. Treatment with low levels of FGF9 (0.2 ng/ml) increased expression of male-specific Dnmt3L and Nanos2 in XY PGCs. Conversely, treatment with high levels of FGF9 (25 ng/ml) suppressed male-specific gene expression and stimulated proliferation of XY PGCs. Western blotting showed that low FGF9 treatment enhanced p38 MAPK (mitogen-activated protein kinase) phosphorylation in the same cells. In contrast, high FGF9 treatment significantly stimulated the ERK (extracellular signal-regulated kinase)1/2 signaling pathway in XY PGCs. We investigated the relationship between the ERK1/2 signaling pathway stimulated by high FGF9 and regulation of PGC proliferation. An ERK1/2 inhibitor (U0126) suppressed the PGC proliferation that would otherwise be stimulated by high FGF9 treatment, and increased Nanos2 expression in XY PGCs. Conversely, a p38 MAPK inhibitor (SB202190) significantly suppressed Nanos2 expression that would otherwise be stimulated by low FGF9 in XY PGCs. Taken together, our results suggest that stage-specific expression of FGF9 in XY gonads regulates the balance between proliferation and differentiation of XY PGCs in a dose-dependent manner.
Identification, molecular characterization and expression analysis of RPL24 genes in three Cucurbitaceae family members: Cucumber, melon and watermelon
(2015-01-01) Baloglu M.C.; Ulu F.; Altunoglu Y.C.; Pekol S.; Alagoz G.; Ese O.
Ribosomal proteins are crucial for the proper growth and development of any organism, including plants. The ribosomal protein L24 (RPL24) is found in the large subunit of the ribosome and is responsible for the stabilization of the peptidyl transferase activity. Although RPL24 gene has been individually identified in different organisms, little is known about the genome-wide survey and expression patterns of R24 genes in Cucurbitaceae family members. We identified seven Cucurbitaceae RPL24 genes from cucumber, melon and watermelon. They were phylogenetically clustered into seven major groups. Gene structure and motif composition are relatively conserved in each group. Three-dimensional homology modelling of RPL24 proteins was performed with higher confidence level. CmRPL24-01 was isolated from melon and characterized at a molecular level. The regulation of ribosomal proteins in melon under drought stress conditions was also studied. The expression of CmRPL24-01 gene increased in melon leaf tissue at 3 h upon polyethylene glycol treatment and showed a gradual induction after 12 h. Our study provided a very useful reference for identification and functional analysis of RPL24 protein members in different plants. In addition, this research indicated a potential usage of ribosomal proteins in response to drought stress.
Immune responses to methanolic extract of black cumin (Nigella sativa) in rainbow trout (Oncorhynchus mykiss)
(2017-08-01) Celik Altunoglu Y.; Bilen S.; Ulu F.; Biswas G.
The immune stimulating effects of the methanolic extract of black cumin (Nigella sativa) in rainbow trout (Oncorhynchus mykiss) was evaluated. Variable concentrations of black cumin methanolic extract [0 (Control), 0.1 and 0.5 g kg−1 of feed] were individually added to the basal diet and rainbow trout was fed for 30 days to assess the innate immune responses and growth performance. Feed conversion ratio significantly decreased in the group fed with 0.5 g kg−1 black cumin extract. Respiratory burst activity was observed to be the highest in the 0.5 g kg−1 black cumin extract fed group. Lysozyme and myeloperoxidase activities were significantly increased in fish of experimental groups compared to control (P < 0.05). TGF-β gene expression increased in black cumin 0.5 g kg−1 treated group. IL-1β and TGF-β gene expressions decreased in black cumin 0.1 g kg−1 administered group. Expression of IL-12 gene diminished in both the experimental groups. There was no significant difference in survival rates between black cumin extract treated fish groups and control (P > 0.05) after challenged with Aeromonas hydrophila. The results indicate that the methanolic extract of black cumin is a stimulator of some innate humoral immune responses, but it is ineffective for cytokine-related gene trancriptions in rainbow trout.
Innate immune and growth promoting responses to caper (Capparis spinosa) extract in rainbow trout (Oncorhynchus mykiss)
(2016-10-01) Bilen S.; Altunoglu Y.C.; Ulu F.; Biswas G.
Cytokine responses, non-specific immune activity and growth promotion effect of dietary caper (Capparis spinosa) supplementation were examined in rainbow trout (Oncorhynchus mykiss). Rainbow trout (12.04 ± 0.71 g) were fed diets containing three doses of caper methanolic extract [0 (Control), 0.1 and 0.5 g kg−1 of feed] for 30 days. At the end of the feeding trial, expression levels of cytokine genes that included IL-1β, IL-8, TGF-β, IL-12p40, TNF-α1 and IL-10 in head kidney was analyzed using qRT-PCR, and blood and serum were collected to determine superoxide anion production (SAP), phagocytic, lysozyme and myeloperoxidase activities. Expression levels of all cytokines, except TNF-α1 were elevated in the 0.1 g kg−1 caper extract fed fish group compared to other groups. In 0.5 g kg−1 caper extract treated fish, only IL-12p40 and IL-10 genes were up-regulated compared to control group fish. SAP was increased in both caper extract treated groups compared to the control, and the highest level was observed in the 0.1 g kg−1 group. Phagocytic activity in both the caper extract treated groups was increased compared to control with no differences observed between those groups. Lysozyme and myeloperoxidase activities were recorded to be the highest in the 0.1 g kg−1 fed fish group compared to other groups. Growth promotion was affected positively when caper doses were increased. Survival rate was significantly higher in 0.1 and 0.5 g kg−1 caper extract treated fish groups compared to control (P < 0.05) after challenged with Aeromonas hydrophila. These results indicate that caper extract stimulates innate immunity through cytokine-mediated responses and promote growth in rainbow trout.