Browsing by Author "Baloglu, Mehmet Cengiz"

Now showing 1 - 20 of 25

Analysis of DNA protection, interaction and antimicrobial activity of isatin derivatives.
(2019-02-01T00:00:00Z) Ganim, Mohamed Abdulhamid; Baloglu, Mehmet Cengiz; Aygun, Aysenur; Altunoglu, Yasemin Celik; Sayiner, Hakan Sezgin; Kandemirli, Fatma; Sen, Fatih
Isatin, thiosemicarbazone and their derivatives have been widely used in biological applications such as antimicrobial, antiviral and anticancer therapies. Herein, eight isatin and thiosemicarbazone derivative compounds were re-synthesized and evaluated for DNA binding analysis including DNA protection studies using plasmid DNA (pUC19) and DNA interaction experiments using calf thymus DNA (CT-DNA). All compounds were also utilized in vitro assay to assess the antimicrobial activity of compounds against different pathogenic bacterial strains. All isatin and thiosemicarbazone derivative compounds exhibited DNA protection activity which ranged from 23.5 to 59.5%. Among them, I3-(N-2-MP)-TSC had the greatest DNA protective activity. For DNA binding analysis, all compounds had the same constant concentration (40 μM), which interacts with CT-DNA. It was also observed that DNA interactions gave a high intrinsic binding constant (Kb = 1.72 × 10 M-9.73 × 10 M). Besides, several derivatives of isatin thiosemicarbazone exhibited significant and selective antibacterial activity with low concentration. These compounds primarily affected Gram-positive bacteria, but were not effective against P. vulgaris and E. coli. The Gram-positive methicillin-resistant S. aureus ATCC 43300 (MRSA) was the most influenced strain by these compounds. It was found that methyphenyl group at isatin was essential for its antibacterial activity for MRSA.
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model.
(2022-08-01T00:00:00Z) Öncül, Ali Burak; Çelik, Yüksel; Ünel, Necdet Mehmet; Baloglu, Mehmet Cengiz
The basic helix loop helix (bHLH) superfamily is a large and diverse protein family that plays a role in various vital functions in nearly all animals and plants. The bHLH proteins form one of the largest families of transcription factors found in plants that act as homo- or heterodimers to regulate the expression of their target genes. The bHLH transcription factor is involved in many aspects of plant development and metabolism, including photomorphogenesis, light signal transduction, secondary metabolism, and stress response. The amount of molecular data has increased dramatically with the development of high-throughput techniques and wide use of bioinformatics techniques. The most efficient way to use this information is to store and analyze the data in a well-organized manner. In this study, all members of the bHLH superfamily in the plant kingdom were used to develop and implement a relational database. We have created a database called bHLHDB (www.bhlhdb.org) for the bHLH family members on which queries can be conducted based on the family or sequences information. The Hidden Markov Model (HMM), which is frequently used by researchers for the analysis of sequences, and the BLAST query were integrated into the database. In addition, the deep learning model was developed to predict the type of TF with only the protein sequence quickly, efficiently, and with 97.54% accuracy and 97.76% precision. We created a unique and next-generation database for bHLH transcription factors and made this database available to the world of science. We believe that the database will be a valuable tool in future studies of the bHLH family.
Biogenic platinum nanoparticles using black cumin seed and their potential usage as antimicrobial and anticancer agent.
(2020-02-05T00:00:00Z) Aygun, Aysenur; Gülbagca, Fulya; Ozer, Lutfiye Yildiz; Ustaoglu, Buket; Altunoglu, Yasemin Celik; Baloglu, Mehmet Cengiz; Atalar, Mehmet Nuri; Alma, Mehmet Hakkı; Sen, Fatih
Herein, the biogenic platinum nanoparticles (Pt NPs) were synthesized by using black cumin seed (Nigella sativa L.) extract as a reducing agent. The biogenic platinum nanoparticles synthesized by black cumin seed extract was characterized in detail by Transmission Electron Microscopy (TEM), UV-vis spectrophotometer, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS). According to TEM analysis, Pt nanoparticles have spherical shapes and sizes between 1-6 nm. Moreover, the biogenic Pt NPs was assessed for its cytotoxicity effect on MDA-MB-231 breast and HeLa cervical cancer lines and their antibacterial effect against selected strains of gram-positive and negative bacteria. The cytotoxicity and bacterial tests showed the effectiveness of biogenic Pt nanoparticles. Dose-dependent toxicity effects were shown in the MDA-MB-231 breast and HeLa cervical cancer lines (IC50: 36.86 μg/mL and 19.83 μg/mL, respectively). In addition, Pt NPs showed high zone diameters against gram-positive and gram-negative bacteria at concentrations of 100 and 500 μg/ml. These results contribute to the development of the pharmaceutical industry as a potential antibacterial and anticancer agent.
Chemical characterization, computational analysis and biological views on Daphne gnidioides Jaub. & Spach extracts: Can a new raw material be provided for biopharmaceutical applications?
(2020-05-13T00:00:00Z) Can, Tevfik Hasan; Tufekci, Enis Fuat; Altunoglu, Yasemin Celik; Baloglu, Mehmet Cengiz; Llorent-Martínez, Eulogio J; Stefanucci, Azzurra; Mollica, Adriano; Cichelli, Angelo; Zengin, Gokhan
The scientific world tends to turn to natural products such as medicinal and aromatic plants because of the inadequacy of commercially available synthetic drugs as antibiotics or anticancer, and their adverse effects on healthy tissues. One of these plants is Daphne gnidioides Jaub. & Spach, which belongs to the Thymelaeaceae family, and there is no data in the literature on its biological activity. This study is aimed to elucidate the chemical profiles and in vitro anticancer, antibacterial and DNA protection and enzyme inhibitory properties of methanol extracts of root, stem, and leaf of D. gnidioides Jaub. & Spach. Polyphenolic components of the extracts were characterized by HPLC-MS/MS. The highest phenolic content was detected in the leaf extract (TIPC = 43.5 ± 0.5 mg/g DE), followed by stem (TIPC = 27.3 ± 0.7 mg/g DE) and root (TIPC = 18.3 ± 0.2 mg/g DE) extracts. Vicenin-2 and 3-O-p-coumaroyl-5-O-caffeoylquinic acid were the main identified compounds in leaf and both root and stem extracts, respectively. The extracts did not show any protective effect on DNA against experimental Fenton's reagent. The minimum inhibitory concentration and the minimum bactericidal concentration values for the root and leaf extracts against tested bacterial strains ranged from 31.25 to 500 μg/mL. After 48 h interaction of the cancer cell lines with the extracts, only the stem extract had significant cytotoxicity on HeLa cells (IC = 86.16 μg/mL). No remarkable activity of the extracts, which was tested against MDA-MB-231, was detected (IC > 1000 μg/mL). These data showed that D. gnidioides Jaub. & Spach stem extract inhibited the survival of HeLa cells in a time-dependent manner. After the treatment of IC concentration of stem extract with HeLa cells, an increase in LC3-II autophagic gene expression was detected. Also, the extracts exhibited significant tyrosinase inhibitory effects which were confirmed by molecular docking. To sum up, the tested extracts could be used as a starting point for the development of new multifunctional drugs.
Chemical fingerprints, antioxidant, enzyme inhibitory, and cell assays of three extracts obtained from Sideritis ozturkii Aytaç & Aksoy: An endemic plant from Turkey.
(2019-07-15T00:00:00Z) Zengin, Gokhan; Uğurlu, Asli; Baloglu, Mehmet Cengiz; Diuzheva, Alina; Jekő, József; Cziáky, Zoltán; Ceylan, Ramazan; Aktumsek, Abdurrahman; Picot-Allain, Carene Marie Nancy; Fawzi Mahomoodally, M
This study was geared towards assessing the possible antioxidant, enzyme inhibitory, and cytotoxic activities of ethyl acetate, methanol, and water extracts of Sideritis ozturkii Aytaç & Aksoy. The phytochemical profiles of the studied extracts were characterised by HPLC-MS/MS. The methanol extract, rich in phenolics (78.04 mg gallic acid equivalent/g), exhibited the strongest antioxidant activities. However, the ethyl acetate extract was the most active extract in the enzyme inhibitory assays. The water extract of S. ozturkii (1 mg/ml, 48 h incubation) slightly inhibited (22%) growth of human breast cancer cell line (MDA-MB-231 cells). On the other hand, the ethyl acetate and methanol extracts showed strong inhibition (98% and 97%, respectively) of MDA-MB-231 cells and caused apoptotic cell death. Scientific data generated from this study further appraises the multiple biological activities of plants belonging to the Sideritis genus. In addition, preliminary evidence gathered from the current investigation advocates for further studies geared towards the preparation of therapeutic formulations from S. ozturkii.
Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon.
(2023-03-01T00:00:00Z) İncili, Çınar Yiğit; Arslan, Büşra; Çelik, Esra Nurten Yer; Ulu, Ferhat; Horuz, Erdoğan; Baloglu, Mehmet Cengiz; Çağlıyan, Ebrar; Burcu, Gamze; Bayarslan, Aslı Ugurlu; Altunoglu, Yasemin Celik
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 Content, Biological and Anticancer Activities of Heracleum humile Extracts Obtained by Ultrasound-Assisted Extraction Method.
(2022-07-01T00:00:00Z) Ocal, Mustafa; Altunoglu, Yasemin Celik; Angeloni, Simone; Mustafa, Ahmed M; Caprioli, Giovanni; Zengin, Gokhan; Paksoy, Mehmet Yavuz; Baloglu, Mehmet Cengiz
As the safety and effectiveness of synthetic drugs remain in doubt, researchers are trying to develop natural medicines from medicinal plants. Herein, ethyl acetate, methanol and water extracts from the Heracleum humile plant were obtained by an ultrasonic-assisted extraction process and the aim was to evaluate some biological effects of the extracts due to the limited data on the pharmacological properties of Heracleum humile in the literature. Weak antibacterial activity was observed on tested bacterial species. The minimum inhibitory concentration and the minimum bactericidal concentration values ranged from 250 to 500 μg/mL. In addition, cytotoxic activity was determined using the MTT test. The strongest findings were determined for ethyl acetate extract on the MDA-MB-231 cell lines at the 48 hour (IC :97.94 μg/mL), followed by the MCF-7 cell lines at the 24 hour (IC :103.9 μg/mL). All extracts of Heracleum humile contained mainly flavonoids, phenolic acids and their derivatives, i. e., well-known compounds that possess numerous biological activities such as antioxidant, anti-inflammatory, anticancer, antimicrobial etc. The study results could provide important information that Heracleum humile could be a potential candidate as a natural enzyme inhibitor. It can be concluded that these extracts could be useful in the elementary step of improving novel plant-derived multifunctional pharmaceuticals.
Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses.
(2021-12-01T00:00:00Z) Arslan, Büşra; İncili, Çınar Yiğit; Ulu, Ferhat; Horuz, Erdoğan; Bayarslan, Aslı Ugurlu; Öçal, Mustafa; Kalyoncuoğlu, Elif; Baloglu, Mehmet Cengiz; Altunoglu, Yasemin Celik
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 () and cucumber () 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. and from cucumber and 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.
CRISPR/Cas9 mediated targeted mutagenesis of LIGULELESS-1 in sorghum provides a rapidly scorable phenotype by altering leaf inclination angle.
(2021-11-01T00:00:00Z) Brant, Eleanor J; Baloglu, Mehmet Cengiz; Parikh, Aalap; Altpeter, Fredy
Sorghum (Sorghum bicolor L. Moench) is one of the world's most cultivated cereal crops. Biotechnology approaches have great potential to complement traditional crop improvement. Earlier studies in rice and maize revealed that LIGULELESS-1 (LG1) is responsible for formation of the ligule and auricle, which determine the leaf inclination angle. However, generation and analysis of lg1 mutants in sorghum has so far not been described. Here, we describe CRISPR/Cas9 mediated targeted mutagenesis of LG1 in sorghum and phenotypic changes in mono- and bi-allelic lg1 mutants. Genome editing reagents were co-delivered to sorghum (var. Tx430) with the nptII selectable marker via particle bombardment of immature embryos followed by regeneration of transgenic plants. Sanger sequencing confirmed a single nucleotide insertion in the sgRNA LG1 target site. Monoallelic edited plantlets displayed more upright leaves in tissue culture and after transfer to soil when compared to wild type. T1 progeny plants with biallelic lg1 mutation lacked ligules entirely and displayed a more severe reduction in leaf inclination angle than monoallelic mutants. Transgene-free lg1 mutants devoid of the genome editing vector were also recovered in the segregating T1 generation. Targeted mutagenesis of LG1 provides a rapidly scorable phenotype in tissue culture and will facilitate optimization of genome editing protocols. Altering leaf inclination angle also has the potential to elevate yield in high-density plantings.
Diverse expression pattern of wheat transcription factors against abiotic stresses in wheat species.
(2014-10-15T00:00:00Z) Baloglu, Mehmet Cengiz; Inal, Behcet; Kavas, Musa; Unver, Turgay
Abiotic stress including drought and salinity affects quality and yield of wheat varieties used for the production of both bread and pasta flour. bZIP, MBF1, WRKY, MYB and NAC transcription factor (TF) genes are the largest transcriptional regulators which are involved in growth, development, physiological processes, and biotic/abiotic stress responses in plants. Identification of expression profiling of these TFs plays a crucial role to understand the response of different wheat species against severe environmental changes. In the current study, expression analysis of TaWLIP19 (wheat version of bZIP), TaMBF1, TaWRKY10, TaMYB33 and TaNAC69 genes was examined under drought and salinity stress conditions in Triticum aestivum cv. (Yuregir-89), Triticum turgidum cv. (Kiziltan-91), and Triticum monococcum (Siyez). After drought stress application, all five selected genes in Kiziltan-91 were induced. However, TaMBF1 and TaWLIP19 were the only downregulated genes in Yuregir-89 and Siyez, respectively. Except TaMYB33 in Siyez, expression level of the remaining genes increased under salt stress condition in all Triticum species. For determination of drought response to selected TF members, publicly available RNA-seq data were also analyzed in this study. TaMBF1, TaWLIP19 and TaNAC69 transcripts were detected through in silico analysis. This comprehensive gene expression analysis provides valuable information for understanding the roles of these TFs under abiotic stresses in modern wheat cultivars and ancient einkorn wheat. In addition, selected TFs might be used for determination of drought or salinity-tolerant and susceptible cultivars for molecular breeding studies.
Evaluation of the Potential Therapeutic Properties of Liquidambar orientalis Oil.
(2023-09-12) Baloglu, Mehmet Cengiz; Yildiz Ozer, Lutfiye; Pirci, Buket; Zengin, Gokhan; Uba, Abdullahi Ibrahim; Celik Altunoglu, Yasemin
Liquidambar orientalis Mill., commonly called the Anatolian sweetgum or Sigla tree, is endemic to southwestern Turkey. It has been historically significant in traditional medicine. In our research, we delved into the therapeutic attributes of its oil, emphasizing its antioxidant, antimicrobial, and antitumor properties. The primary chemical constituent of the gum is styrene, accounting for 78.5%. The gum demonstrated antioxidant capabilities in several assays, including in 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), cupric reducing antioxidant capacity (CUPRAC) and ferric reducing antioxidant power (FRAP). It displayed bactericidal actions against various gram-positive bacteria, such as Staphylococcus aureus, and gram-negative strains, including Escherichia coli. Additionally, the oil showcased potent antitumor effects against breast (MDA-MB-231), lung (A549), and prostate (PC3) cancer cell lines. These effects were found to be both time- and dose-dependent. L. orientalis Mill. oil showed the best antitumor activity against breast, lung, and prostate cancer cell lines after the 24 h and 48h treatment. Its oil might induce autophagy in the PC3 prostate cancer cell line, whereas its cytotoxicity against MDA-MB-231 and A549 cancer cell lines might not be correlated with autophagy or apoptosis pathways. In conclusion, the oil from the Sigla tree offers promising therapeutic potential and warrants further exploration.
Exploring of the ameliorative effects of Nerium (Nerium oleander L.) ethanolic flower extract in streptozotocin induced diabetic rats via biochemical, histological and molecular aspects.
(2023-03-10T00:00:00Z) Battal, Abdulhamit; Dogan, Abdulahad; Uyar, Ahmet; Demir, Abdulbaki; Keleş, Ömer Faruk; Celik, Ismail; Baloglu, Mehmet Cengiz; Aslan, Ali
Nerium oleander L. is ethnopharmacologically used for diabetes. Our aim was to investigate the ameliorative effects of ethanolic Nerium flower extract (NFE) in STZ-induced diabetic rats.
Exploring the Nutraceutical Potential of Dried Pepper L. on Market from Altino in Abruzzo Region.
(2020-05-08T00:00:00Z) Della Valle, Alice; Dimmito, Marilisa Pia; Zengin, Gokhan; Pieretti, Stefano; Mollica, Adriano; Locatelli, Marcello; Cichelli, Angelo; Novellino, Ettore; Ak, Gunes; Yerlikaya, Serife; Baloglu, Mehmet Cengiz; Celik Altunoglu, Yasemin; Stefanucci, Azzurra
Sweet pepper is a typical type of from Abruzzo region, recognized as a traditional and local product, traditionally cultivated in the town of Altino (Abruzzo region, Italy). The aim of this study is to compare the sweet type of peppers from Altino with the hot pepper cultivated in the same area, in order to delineate their different phytochemical and biological profiles in vitro and in vivo. In this study, we elucidated their phytochemical composition, fatty acids composition and phenolic/flavonoid contents in extracts. Then antioxidant and enzyme inhibition assays were performed to evaluate their biological properties, together with in vitro cell assay and in vivo anti-inflammatory activity. Microwave (1000 mg/mL) extract of hot pepper showed the best inhibition value on in vitro cell growth assay; in fact, the number of survived cells was about 20% and 40% for microwave and Soxhlet extracts, respectively. In vivo anti-inflammatory assay revealed good activity for both species, which, when associated with in vitro cell inhibition results, could explain the protective effect on human prostatic hyperplasia.
Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects.
(2022-01-28) Baloglu, Mehmet Cengiz; Celik Altunoglu, Yasemin; Baloglu, Pinar; Yildiz, Ali Burak; Türkölmez, Nil; Özden Çiftçi, Yelda
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 analysis of the bZIP transcription factors in cucumber.
(2014-04-23) Baloglu, Mehmet Cengiz; Eldem, Vahap; Hajyzadeh, Mortaza; Unver, Turgay
bZIP proteins are one of the largest transcriptional regulators playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of recently published draft genome sequence of Cucumis sativus, no comprehensive investigation of these family members has been presented for cucumber. We have identified 64 bZIP transcription factor-encoding genes in the cucumber genome. Based on structural features of their encoded proteins, CsbZIP genes could be classified into 6 groups. Cucumber bZIP genes were expanded mainly by segmental duplication rather than tandem duplication. Although segmental duplication rate of the CsbZIP genes was lower than that of Arabidopsis, rice and sorghum, it was observed as a common expansion mechanism. Some orthologous relationships and chromosomal rearrangements were observed according to comparative mapping analysis with other species. Genome-wide expression analysis of bZIP genes indicated that 64 CsbZIP genes were differentially expressed in at least one of the ten sampled tissues. A total of 4 CsbZIP genes displayed higher expression values in leaf, flowers and root tissues. The in silico micro-RNA (miRNA) and target transcript analyses identified that a total of 21 CsbZIP genes were targeted by 38 plant miRNAs. CsbZIP20 and CsbZIP22 are the most targeted by miR165 and miR166 family members, respectively. We also analyzed the expression of ten CsbZIP genes in the root and leaf tissues of drought-stressed cucumber using quantitative RT-PCR. All of the selected CsbZIP genes were measured as increased in root tissue at 24th h upon PEG treatment. Contrarily, the down-regulation was observed in leaf tissues of all analyzed CsbZIP genes. CsbZIP12 and CsbZIP44 genes showed gradual induction of expression in root tissues during time points. This genome-wide identification and expression profiling provides new opportunities for cloning and functional analyses, which may be used in further studies for improving stress tolerance in plants.
Genome-wide identification and comparative expression analysis of genes in watermelon and melon genomes.
(2017-01-01T00:00:00Z) Celik Altunoglu, Yasemin; Baloglu, Mehmet Cengiz; Baloglu, Pinar; Yer, Esra Nurten; Kara, Sibel
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 genes from watermelon () and 61 genes from melon () 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 gene expansion in watermelon. Maximum gene ontology of genes was observed with poplar genes. For evaluation of tissue specific expression patterns of and genes, publicly available RNA-seq data were analyzed. The expression analysis of selected genes in root and leaf tissues of drought-stressed watermelon and melon were examined using qRT-PCR. Among them, --- genes were quickly induced after drought application. Therefore, they might be considered as early response genes for water limitation conditions in watermelon. In addition, -- 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.
Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean.
(2015-11-27) Kavas, Musa; Kizildogan, Aslihan; Gökdemir, Gökhan; Baloglu, Mehmet Cengiz
Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.
Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones.
(2018-12-15T00:00:00Z) Yer, Esra Nurten; Baloglu, Mehmet Cengiz; Ayan, Sezgin
Heat shock proteins (Hsps) play a key role for regulation of the changes during different stress conditions including salinity, drought, heavy metal and extreme temperature. Molecular based studies on the response mechanisms of forest trees to abiotic stresses started in 2006 when Populus trichocarpa genome sequence was completed as a model tree species. In recent years, bioinformatic analyzes have been carried out to determine functional gene regions of tree species. In this study, sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members were identified in poplar genome. Some bioinformatics analyses were conducted, such as: identification of DNA/protein sequences, chromosomal localization, gene structure, calculation of genomic duplications, determination of phylogenetic groups, examination of protected motif regions, identification of gene ontology categories, modeling of protein 3D structure, determination of miRNA targeting genes, examination of sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members in transcriptome data during salinity stress. As a result of bioinformatic analyzes made on P. trichocarpa genome; 60, 145, 49, 34, 12 and 90 genes belonging to members of sHsp, Hsp40, Hsp60, Hsp70, Hsp90 and Hsp100 protein families were firstly defined within the scope of this study. A total of 390 genes belonging to all Hsps gene families were characterized using different bioinformatics tools. In addition, salinity stress was applied to Populus tremula L. (Samsun) naturally grown in Turkey, Hybrid poplar species I-214 (Populus euramericana Dode. Guinier) and Black Poplar species (Populus nigra L.), Geyve and N.03.368.A clones. The expression levels of the selected Hsps genes were determined by the qRT-PCR method. After salt stress application in various poplar clones, expression levels of genes including PtsHsp-11, PtsHsp-21, PtsHsp-36, PtHsp40-113, PtHsp40-117, PtHsp60-31, PtHsp60-33, PtHsp60-38, PtHsp60-49, PtHsp70-09, PtHsp70-12, 33, PtHsp90-09, PtHsp90-12, PtHsp100-21, and PtHsp100-75 were increased. The role of the Hsps genes during salt stress has been revealed. Together with detailed bioinformatics analyses, gene expression analysis greatly contributes to understand functions of these gene family members. This research serves as a blueprint for future studies and offers a significant clue for the further study of the functions of this important gene family. Moreover, determined genes in this study can also be used for cloning studies in agricultural practices.
Investigation of chemical profile, biological properties of Lotus corniculatus L. extracts and their apoptotic-autophagic effects on breast cancer cells.
(2019-09-10T00:00:00Z) Yerlikaya, Serife; Baloglu, Mehmet Cengiz; Diuzheva, Alina; Jekő, József; Cziáky, Zoltán; Zengin, Gokhan
This study aimed to reveal chemical profiles and biological activities of ethyl acetate (EA), methanol (MeOH), and water extracts of Lotus corniculatus. Ethnobotanical reports have indicated the importance of phytochemical properties of the genus Lotus. In this study, the effects of medicinal plant extracts on antioxidant (DPPH, ABTS, CUPRAC, FRAP, phosphomolybdenum, and metal chelating assays), enzyme inhibitory (on cholinesterase, tyrosinase, a-amylase and a-glucosidase), DNA protection and anticancer properties (including anti-proliferative, cell death and telomerase activity marker gene analysis, apoptotic DNA fragmentation analysis, cell migration test) were evaluated. According to chemical analysis, quercetin derivatives geraldol, isorhamnetin and kaempferol-O-coumaroylhexoside-O-deoxyhexoside isomers were dominant in the extracts. MeOH extracts showed the highest total flavonoids capacity with 21.13 mg RE/g. EA extract showed the strongest anti-amylase activity among the tested extracts. Water extract had the most protective activity against plasmid DNA. To indicate cell survival, MTT test was performed against human MCF-7 and MDA-MB-231 breast cancer cells. Half-maximal inhibitory concentration for cells were calculated and used for detection of mechanisms behind the cancer cell death. EA extract showed up-regulation of Bax proapoptotic gene and apoptotic DNA fragmentation activity on highly invasive MDA-MB-231 cells. Beclin-1 and LC3-II autophagy genes were higly expressed after treatment of MCF-7 cells with EA extracts. EA and MeOH extracts inhibited cell migration ability of both cancer cells. Linoleamide, was dominant component in EA extract and caused apoptosis on MDA-MB-231 breast cancer cells via increasing intranuclear Ca². The detailed mechanism behind the anticancer properties should be further investigated.
Investigations into the therapeutic potential of Asphodeline liburnica roots: In vitro and in silico biochemical and toxicological perspectives.
(2018-10-01T00:00:00Z) Locatelli, Marcello; Yerlikaya, Serife; Baloglu, Mehmet Cengiz; Zengin, Gokhan; Altunoglu, Yasemin Celik; Cacciagrano, Francesco; Campestre, Cristina; Mahomoodally, Mohamad Fawzi; Mollica, Adriano
This study aims to establish the biological and chemical profile of Asphodeline liburnica (Scop.) Rchb. root. The antioxidant, antimicrobial, enzyme inhibitory, DNA protection, apoptotic DNA ladder fragmentation analysis, and anti-proliferative of A. liburnica were established using standard assays. In silico study was also performed to understand interactions between quantified anthraquinones and key enzymes of clinical relevance. Total phenolic and flavonoid contents were found to be 9.67 mgGAE/g and 1.48 mgRE/g extract, respectively. Chrysophanol was detected as a major anthraquinone. The extract exhibited radical scavenging ability against DPPH and ABTS with values of 13.23 and 66.99 mgTE/g extract, respectively. Good inhibitory activity against tyrosinase was recorded. In silico experiments showed that the anthraquinones were able to establish coordinative bonds with the copper atoms present in the enzymatic cavity of tyrosinase. MTT cell viability test on MDA-MB-231 cells showed that at 0.1 and 1 μg of extracts induced anti-proliferative effect. Apoptotic DNA fragmentation analysis indicated nuclear condensation resulting in DNA fragmentation, which exhibited apoptotic cell death in the presence of A. liburnica. This study has provided insights on the potential usage of A. liburnica which could open new avenues for research and stimulate future interest for the development of safe novel biopharmaceuticals.