Browsing by Author "Celik Altunoglu Y."

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Anticancer, antimicrobial, and DNA protection analysis of novel 2,4-dihydroxyquinoline dyes
(2018-10-01) Şener N.; Mohammed H.J.A.; Yerlikaya S.; Celik Altunoglu Y.; Gür M.; Baloglu M.C.; Şener İ.
A new series of 2,4-dihydroxyquinoline derived disazo dyes has been synthesized by the reaction of 5-amino-4-phenylazo-3-methyl-1H-pyrazole derivatives with 2,4-dihydroxyquinoline. The structures of the obtained dyes were identified by various spectrophotometric methods such as FT-IR, 1H-NMR, and elemental analysis. The synthesized compounds were also examined for different biological activities, including DNA protection, antimicrobial, and anticancer activities. Compound 3b was found most effective on Gram-positive bacteria. A DNA protection assay was applied to all compounds, and it was found that compounds 3h and 3j had a high capacity for binding to DNA. Besides, compounds 3h and 3j showed cytotoxicity against HeLa and PC3 cancer cell lines. These compounds could potentially be used as drugs or drug additives based on their effects on bacterial and cancer cell lines.
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.
Comparative identification, characterization, and expression analysis of bZIP gene family members in watermelon and melon genomes
(2019-03-02) Unel N.M.; Cetin F.; Karaca Y.; Celik Altunoglu Y.; Baloglu M.C.
The family of basic leucine zipper (bZIP) transcription factors plays diverse crucial roles in numerous biological processes. Despite the identification of bZIP genes in several plants, to our knowledge, bZIP members in watermelon and melon are yet to be comprehensively investigated. The genomes of watermelon and melon encode 59 ClabZIP and 75 CmbZIP putative genes, respectively. Both bZIP protein family members were phylogenetically grouped into seven subfamilies. The majority of bZIP genes in the same subfamily shared similar gene structures and conserved motifs. Chromosome distribution and genetic analysis revealed that 21 duplication events between ClabZIP genes and 106 duplication events between CmbZIP genes have occurred. Further, the three-dimensional structure and functional annotation of bZIP proteins was predicted. For evaluating the expression patterns of ClabZIP and CmbZIP genes, RNA-seq data available in public databases were analyzed. The expression profiles of selected ClabZIP and CmbZIP genes in root and leaf tissues of drought-stressed watermelon and melon were also examined using qRT-PCR. ClabZIP-57, CmbZIP-52, and CmbZIP-31 genes exhibited the highest expression levels after stress exposure in leaf and root tissues. Gene identification studies like the present study offer new perspectives in the analysis of bZIP protein family members and their functions in plants.
Comprehensive approaches on chemical composition and biological properties of Daphne pontica L. extracts
(2022-01-01) Celik Altunoglu Y.; Can T.H.; Tufekci E.F.; Altunoglu B.D.; Baloglu M.C.; Llorent-Martínez E.J.; Zengin G.
The genus Daphne presents great interest as a valuable source of natural agents in traditional medicine of various countries, including Turkey. In the current work, we investigated the phytochemical composition and biological properties of Daphne pontica L. extracts. Methanol extracts of roots, stems and leaves were prepared. The chemical characterization was performed by HPLC-ESI-MSn, observing that flavonoids and phenolic acids were the main compounds. Biological properties were studied in terms of antimicrobial, DNA protection, anticancer, and enzyme inhibitory properties (cholinesterases, tyrosinase, amylase and glucosidase). Methanol extracts of roots, leaves, and stems of D. pontica had antimicrobial effects against a broad range of bacteria. In addition, methanol extract of roots of D. pontica exhibited a promising anticancer activity that was shown to be dose- and time-dependent for HeLa cells with an IC50 value of 203.9 μg/mL. Generally, the leaf extracts exhibited the best enzyme inhibitory properties on the tested enzymes. According to our results, D. pontica might be regarded as a valuable source of natural agents to combat cancer, infectious diseases, and metabolic diseases.
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family
(2023-06-01) Kök B.Ö.; Celik Altunoglu Y.; Öncül A.B.; Karaci A.; Cengiz Baloglu M.
Expansins, which are plant cell wall loosening proteins associated with cell growth, have been identified as a multigene family. Plant expansin proteins are an important family that functions in cell growth and many of developmental processes including wall relaxation, fruit softening, abscission, seed germination, mycorrhiza and root nodule formation, biotic and abiotic stress resistance, invasion of pollen tube stigma and organogenesis. In addition, it is thought that increasing the efficiency of plant expansin genes in plants plays a significant role, especially in the production of secondary bioethanol. When the studies on the expansin genes are examined, it is seen that the expansin genes are a significant gene family in the cell wall expansion mechanism. Therefore, understanding the efficacy of expansin genes is of great importance. Considering the importance of this multigene family, we aimed to create a comprehensively informed database of plant expansin proteins and their properties. The expansin gene family database provides comprehensive online data for the expansin gene family members in the plants. We have designed a new website accessible to the public, including expansin gene family members in 70 plants and their features including gene, coding and peptide sequences, chromosomal location, amino acid length, molecular weight, stability, conserved motif and domain structure and predicted three-dimensional architecture. Furthermore, a deep learning system was developed to detect unknown genes belonging to the expansin gene family. In addition, we provided the blast process within the website by establishing a connection to the NCBI BLAST site in the tools section. Thus, the expansin gene family database becomes a useful database for researchers that enables access to all datasets simultaneously with its user-friendly interface. Our server can be reached freely at the following link (http://www.expansingenefamily.com/).
Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects
(2022-06-28) Baloglu M.C.; Celik Altunoglu Y.; Baloglu P.; Yildiz A.B.; Türkölmez N.; Özden Çiftçi Y.
Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.
Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes
(2017-01-01) Celik Altunoglu Y.; Baloglu M.C.; Baloglu P.; Yer E.N.; Kara S.
Late embryogenesis abundant (LEA) proteins are large and diverse group of polypeptides which were first identified during seed dehydration and then in vegetative plant tissues during different stress responses. Now, gene family members of LEA proteins have been detected in various organisms. However, there is no report for this protein family in watermelon and melon until this study. A total of 73 LEA genes from watermelon (ClLEA) and 61 LEA genes from melon (CmLEA) were identified in this comprehensive study. They were classified into four and three distinct clusters in watermelon and melon, respectively. There was a correlation between gene structure and motif composition among each LEA groups. Segmental duplication played an important role for LEA gene expansion in watermelon. Maximum gene ontology of LEA genes was observed with poplar LEA genes. For evaluation of tissue specific expression patterns of ClLEA and CmLEA genes, publicly available RNA-seq data were analyzed. The expression analysis of selected LEA genes in root and leaf tissues of drought-stressed watermelon and melon were examined using qRT-PCR. Among them, ClLEA-12-17-46 genes were quickly induced after drought application. Therefore, they might be considered as early response genes for water limitation conditions in watermelon. In addition, CmLEA-42-43 genes were found to be up-regulated in both tissues of melon under drought stress. Our results can open up new frontiers about understanding of functions of these important family members under normal developmental stages and stress conditions by bioinformatics and transcriptomic approaches.
Identification and expression analysis of LEA gene family members in cucumber genome
(2016-11-01) Celik Altunoglu Y.; Baloglu P.; Yer E.N.; Pekol S.; Baloglu M.C.
LEA (late embryogenesis abundant) proteins are firstly discovered in seeds and then identified in vegetative tissues of different plant species. They are mainly regulated under abiotic stress conditions. Although genome wide studies of different gene family members have been performed in cucumber, there is no such a study for LEA genes. We have identified 79 LEA genes in the cucumber genome. Based on phylogenetic analysis, CsLEA genes could be classified into seven groups in which structural motifs are relatively conserved. Tandem duplications play an important role in cucumber genome for LEA gene expansion. Orthologous and chromosomal relationships of CsLEA genes were observed based on comparative mapping analysis with other species. The in silico micro-RNA (miRNA) target analyses indicated that 37 CsLEA genes were targeted by different miRNAs, especially mir854 and mir414 are the most abundant identified ones. Public available RNA-seq data were analyzed for expression analysis of CsLEA genes in different tissues of cucumber. According to genome-wide expression analysis, nine CsLEA genes showed higher expression profiles in all tissues. The expression profiles of ten CsLEA genes in the root and leaf tissues of drought-stressed cucumber were examined using qRT-PCR. Among them, CsLEA-54 induced after stress application in leaf and root tissues and might provide adaptation to drought stress for cucumber. CsLEA-09, CsLEA-32 and CsLEA-57 genes responded to drought after 3 h later and might be considered as early response genes to water limitation. This research could help us to improve understanding of contribution of CsLEAs to drought tolerance in cucumber.
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.
Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses
(2023-01-01) Faris Abdulkhadum Al-Mamoorı D.; Celik Altunoglu Y.; Horuz E.; Özkan Kök B.