Aim of study: It was aimed to identify and characterize Hsp genes in jujube genome using genomics methods.
Material and method: Protein sequences of jujube Hsp genes were obtained from NCBI ...databases. GSDS program was used to detect of exon-intron sites. To define the conserved motifs and estimated 3D-structures, Hsp proteins were used in the MEME-SUITE and PHYRE2 program, respectively. miRNAs targeting ZjuHsp transcripts were identified using the psRNATarget Server database. The gene annotations of Hsp proteins were presented by Blast2GO program. Sequence alignment was performed with ClustalW software, and then the phylogenetic tree was drawn using MEGAX program.
Main results: A total of 474 genes were defined in the jujube genome. The amino acid length of the Hsp proteins changes from 75 aa to 2577 aa. The estimated 3-D structure of the ZjuHsp proteins revealed the dominance of the α-helix structure. Phylogenetic tree was constructed to detect evolutionary relationships revealed the eight major groups of the ZjuHsp100 and ZjuHsp60. ZjuHsp proteins could be mainly found in cell parts, membranes, and organelles. It was determined that the ZjuHsp100 genes was targeted by 313 miRNAs.
Highlights: This study helps the researchers who would like to comparative and functional genomic studies.
Çalışmanın amacı : Bu çalıĢmada, genomic yöntemler kullanarak hünnap genomunda yer alan Hsp genlerini tanımlamak ve karakterize etmek amaçlanmıĢtır.
Materyal ve yöntem : NCBI veritabanı kullanılarak Hsp genlerinin protein dizileri elde edilmiĢtir. Genlerin ekzon-intron bölgelerinin tespiti, GSDS program ile yapılmıĢtır. Hsp proteinlerinin korunmuĢ motiflerini ve tahmini üç boyutlu yapılarını tanımlamak için sırasıyla MEME-SUITE ve PHYRE2 programı kullanılmıĢtır. Hsp transkriptlerini hedefleyen miRNA'lar, psRNATarget Server veritabanı kullanılarak tanımlanmıĢtır. Hsp proteinlerinin moleküler fonksiyonu, hücresel bileĢeni ve biyolojik fonksiyonları Blast2GO program ile sunulmuĢtur. Hsp proteinlerinin evrimsel iliĢkilerini belirlemek amacı ile ClustalW yazılımı ile dizi hizalaması yapılmıĢ ve ardından MEGAX program ile filogenetik ağaç çizilmiĢtir.
Temel sonuçlar: Hünnap genomunda toplam 474 gen tanımlanmıĢ ve genler çoğunlukla 1. ve 2. kromozomda dağılım göstermiĢtir. Hsp proteinlerinin amino asit uzunluğu 75 aa (ZjuHsp100-117) ile 2577 aa (ZjuHsp40-104 ve ZjuHsp40-157) arasında değiĢim göstermiĢtir. ZjuHsp proteinlerinin tahmini üç boyutlu yapısında α-sarmal yapısının baskın olduğu görülmüĢtür. Proteinlerin evrimsel iliĢkilerini saptamak için oluĢturulan filogenetik ağaçta, ZjuHsp100 ve ZjuHsp60 grup proteinlerin sekiz ana gruba ayrıldığı gözlenmiĢtir. ZjuHsp proteinlerinin esas olarak hücre kısımlarında, zarlarda, ve organellerde bulunduğu tespit edilmiĢtir. ZjuHsp transkriptlerini hedef alan miRNA'lardan 313'ünün ZjuHsp100 genlerini hedeflediği bulunmuĢtur.
Araştırma vurguları : Bu çalıĢma, karĢılaĢtırmalı ve fonksiyonel genomic çalıĢmalar yapmak isteyen araĢtırmacılara yardımcı olmaktadır.
Anahtar Kelimeler: Isı şoku Proteinleri (Hsp), Ziziphus jujuba, Genom Analizi, Gen Ontoloji Analizi, Filogenetik Ağaç
Ethnobotanical evidences report the use of Rhododendron luteum Sweet (Ericaceae) in traditional medicinal systems. However, R. luteum has been associated to the occurrence of ‘mad honey’ poisoning. ...In the present study, the ethyl acetate, methanol, and water extracts of R. luteum were investigated for their in vitro antioxidant, enzyme inhibition, and cytotoxic properties. The cytotoxicity of R. luteum extracts on A549 lung cancer cell line was evaluated using MTT cell viability assay. Besides, HPLC-ESI-MSn approach was employed to elucidate the secondary metabolite profiles of R. luteum in order to establish any structure-activity relationship. Methanol and water extracts of R. luteum possessed highest radical scavenging and reducing properties while the ethyl acetate extract showed highest metal chelating properties. In terms of enzyme inhibition, the methanol and ethyl acetate extracts of R. luteum, possessing epigallocatechin, were active inhibitors of cholinesterase enzymes, α-glucosidase, and tyrosinase. Water extract caused growth inhibition of A549 cells with 207.2 μg/ml IC50 value. Though R. luteum has received little scientific attention due to the occurrence of grayanotoxins in the plant, however, data presented in this work shows promising biological activity of R. luteum and highlighted its role as a potential source of antioxidant and key enzyme inhibitors.
•Biological properties and chemical profiles of Rhododendron luteum extracts were investigated using in vitro assays.•Monomers and dimers of phenolic acids in free and glycosylated forms were identified in Rhododendron luteum extracts.•Water extract exhibited antiproliferative action against A549 lung cancer cells.•Ethyl acetate and methanol extracts of Rhododendron luteum were active against the tested enzymes.
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.
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.
•Heat shock proteins (Hsps) are group of proteins found in living organisms and called as stress proteins.•A total of 390 Hsps genes were identified in the Populus trichocarpa genome.•The possible functions and roles of Hsps genes were determined using bioinformatics tools.•Hsps genes were differently induced by salt stress in different poplar clones because of genotypic variation.
•The green synthesis of Pt NPs by using Black Cumin Seed Extract,•Characterization of biogenic Pt NPs by XRD, XPS, TEM, HRTEM, and UV–vis methods•High antibacterial activity of Pt NPs against ...gram-positive and gram-negative bacteria•The very efficient inhibition of proliferation of MDA-MB-231 and HeLa cells.
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.
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.
Broad-spectrum antibiotics have been widely used in the treatment of many systemic and local infections in humans and animals. Herein, we aimed to determine the synergistic and antagonistic effects ...of phenylalanine with antibiotics cefoxitin, amoxicillin, vancomycin, lincomycin, and bacitracin against 14 pathogenic bacteria. The effect of antibiotics, either alone or in combination with this biomolecular liquid, was tested using the disk diffusion method against different bacteria. The addition of phenylalanine to antibiotic disks directly affected their antimicrobial activity. All the antibiotics used did not show any antimicrobial activity against
Staphylococcus haemolyticus
when used alone. However, in combination with phenylalanine, each antibiotic inhibited the growth of
S. haemolyticus
. The use of this biomolecular liquid together with amoxicillin and vancomycin also increased the antimicrobial activity against
Enterococcus durans
. The use of phenylalanine in combination with antibiotics also resulted in antagonistic effects on some pathogens. Further, the effects of antibiotics in combination with phenylalanine on different bacterial pathogens were investigated in vitro. Results provide valuable information to further our understanding of the molecular mechanism of action of antibiotics and to improve their efficacy against bacterial pathogens.
Drought is crucial abiotic stress that limits growth and causes a|yield reduction in wheat. So, the identification of susceptible and tolerant wheat cul-tivars to drought is critical for breeders. In ...this study, physiological and biochemical responses against drought stress were investigated in wheat varieties, Siyez (Triticum monococcum)^ Kiziltan-91 (Triticum turgid urn) and Yüregir-89 (Triticum aestivum) possessing different ploidy levels. Some growth. physiological parameters (membrane permeability, malondialdehyde, H2O2, proline and ascorbic acid) and antioxidant enzyme activity (SOD, CAT, APX and GPX) analyses were performed. The first effect of drought was the increase in root lengths for all species. Ascorbic acid and proline amount raised in roots and shoots at a maximum in Yüregir-89 and at a minimum in Siyez. An increase in the CAT activity was observed in the roots of Yüregir-89 and in the leaves of Kiziltan-91. Similar defensive patterns of SOD and GPX enzymes were monitored in Yüregir-89 and Kiziltan-91 tissues. Genotypic variation arisen from ploidy level contributed by various parameters was also determined by principal component (PCA) analysis under drought stress. As a result of all analyses, Kiziltan-91 and Yüregir-89 wheat varieties could be considered as resistant to drought and Siyez wheat was susceptible to drought. The possible explanations for this might be strong enzymatic and non-enzymatic antioxidant defense mechanisms and high ploidy levels mechanisms in Kiziltan-91 and Yüregir-89 varieties. This study has the potential to become a reference source for studies of the identification of wheat species with a high survival rate under drought in the future.
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