Browsing by Author "Özkale, E"

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    Progresses on Metagenomic Airbiome Studies
    Özkale, E
    The term microbiome refers to the collective genome of the microbial communities living in various environments/habitats, and recently, the understanding of microbiome have been significantly enhanced by metagenomic studies. The data at hand regarding marine and soil-related microbial communities is much more than that of the air, which is typically not colonized, and the number of publications sharp contrasts to those of air. Aerosols of biological origin (bioaerosols) are a subset of atmospheric particulate matter (PM), which are emitted directly from the biosphere into the atmosphere, and play a vital role in the system of theEarth, particularly in the interactions between atmosphere, biosphere, climate and public health. However, these particles could either be the direct cause of epidemics of infectious diseases or noninfectious diseases (e.g. hypersensitivity to aeroallergens). These bioparticles emitted by humans or re-suspended from surfaces in indoor environments are also challenging for infection control and safety. It is estimated that humans emit approximately 106 particles per hour into the surrounding air under seated conditions. The sources, abundance, composition and effects of bioaerosols and the atmospheric microbiome are not yet well characterized; however, there is a continually increasing number of published studies. In this review, current progresses and conducted studies on airborne metagenomics were described and the health effects of aerosols to global perspective were overviewed.
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    Trichoderma atroviride triggers alterations at epigenetics, transcripts, oxidative stress, and apoptosis levels on Fusarium graminearum
    Yörük, E; Özkale, E; Sefer, Ö; Özsoy, E
    Fusarium graminearum is a phytopathogenic fungus causing head blight and crown rot diseases of cereals worldwide. The use of organisms with antagonistic effects against F. graminearum is one of the promising disease management strategies. In this study, the biocontrol agent potential of Trichoderma atroviride against F. graminearum was tested. The radial growth rate and the cell proliferation capacities of F. graminearum PH-1 treated with T. atroviride TR8 (FGvsTA) decreased in comparison to F. graminearum not treated with T. atroviride (FGc). The decrease in linear growth rate (LGR) and cytotoxicity values were as %50 and %45, respectively. Genomic template stability (GTS) and epigenetic alterations were investigated via RAPD and CRED-RA methods. GTS was recorded as 66.6%, and polymorphism % for MspI and HapII digested FGvsTA set were as 26% and 13.88%. In gene expression analysis, alterations in genes related to oxidative stress (cat), apoptosis-like process (mst20), and deoxynivalenol production (tri4) were revealed. While expression of gene mst20 was upregulated, downregulation in cat and tri4 expressions were recorded (p < 0.05). Fluorescence microscopy analysis, including acridine orange/ethidium bromide (Ao/Eb) and dichlorofluorescein diacetate (DCF-DA) also confirmed the presence of apoptosis and oxidative stress in FGvsTA. This is the first report with findings that T. atroviride could strongly affect F. graminearum growth in different ways, including physiological, genomics, epigenetics, oxidative stress, and apoptosis-like process levels.
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    Trichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profiling
    Özkale, E; Yörük, E; Budak, M; Korkmaz, EM
    The use of Trichoderma spp. offers an ecologically friendly tool for the struggle with mycotoxigenic Fusarium spp. Here, the alterations in transcriptome level were investigated in 6-day-old Fusarium graminearum cultures treated with Trichoderma atroviride and nontreated with T. atroviride (FGc), using whole transcriptome sequencing to better understand the associated biological processes. Transcriptome analysis indicated a total of 55 up-regulated genes and 728 down-regulated genes with p(adj) < 0.05. Enrichment analysis revealed that the up-regulated genes were related to fatty acid biosynthesis, AMP-dependent biosynthesis, amino acid recognition/activation processes and secondary metabolite production, whereas down-regulated genes were involved in amino acid synthesis, oxidation-reduction processes, metal ion-binding and metabolic/catalytic activities. Among the down-regulated genes, the expression of pigmentation-related genes such as aurO, gip1 and aurR2 was remarkable. Similarly, the expression levels of key enzyme-coding genes involved in deoxynivalenol mycotoxin production were significantly decreased in the range of -1.77 and -2.94. For up-regulated genes, nonribosomal peptide synthetase and polyketide synthase genes were notably distinguished from the remaining down-regulated genes as these genes can be involved in biosynthesis of common secondary metabolites. The results clearly emphasize that T. atroviride repressed the biosynthesis of primary metabolites in F. graminearum while simultaneously up-regulating the expression of genes involved in the synthesis of secondary metabolites. This is the first report showing how T. atroviride leads to transcriptome alterations and the findings suggest that T. atroviride could serve as an effective fungus by employing a wide variety of strategies against phytopathogenic fungi.
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    Determining the biocontrol capacities of Trichoderma spp. originating from Turkey on Fusarium culmorum by transcriptional and antagonistic analyses
    Sefer, Ö; Özsoy, E; Yörük, E; Özkale, E
    In this study aiming to investigate potential fungal biocontrol agents for Fusarium culmorum, several isolates of Trichoderma spp. were evaluated for their antagonistic effects by means of transcriptional analyses. At first, 21 monosporic Trichoderma spp. isolates were obtained from natural wood debris and wood area soils in Manisa, Turkey. Trichoderma spp. Isolates were identified as belonging to four different species (T. atroviride, T. harzianum, T. koningii, and T. brevicompactum) by tef1-alpha sequencing. Then, the linear growth rate (LGR) of each species was calculated and determined to be in a range between 13.22 +/- 0.71 mm/day (T. atroviride TR2) and 25.06 +/- 1.45 mm/day (T. harzianum K30). Inter-simple sequence repeat (ISSR) genotyping validated the tef1-alpha sequencing results by presenting two sub-clusters in the dendrogram. We determined the genetically most similar (TR1 & TR2; 97.77%) and dissimilar (K9 & K17; 40.40%) individuals belonging to the same and different species, respectively. Dual sandwich culture tests (which are useful for antagonism studies) revealed that T. harzianum K21 (the least suppressive) and T. brevicompactum K26 (the most suppressive) isolates suppressed F. culmorum with growth rates of 3% and 46%, respectively. Expressions of genes previously associated with mycoparasitism-plant protection-secondary metabolism (nag1, tgf-1, and tmk-1) were tested by quantitative real-time polymerase chain reaction (qRT-PCR) in both those isolates. While there were no significant differences (p>0.05) in expression that were present in the K21 isolate, those three genes were upregulated with fold change values of 2.69 +/- 0.26 (p<0.001), 2.23 +/- 0.16 (p<0.001), and 5.38 +/- 2.01 (p<0.05) in K26, meaning that the presence of significant alteration in the physiological processes of the fungus. Also, its mycoparasitism potential was tested on Triticum aestivum L. cv Basribey in planta, which was infected with the F. culmorum FcUK99 strain. Results of the trials, including specific plant growth parameters (weight or length of plantlets), confirmed the mycoparasitic potential of the isolate. It can be concluded that (i) nag1, tgf-1, and tmk-1 genes could be approved as reliable markers for evaluation of BCA capacities of Trichoderma spp. and (ii) the T. brevicompactum K26 strain can be suggested as a promising candidate for combating in F. culmorum diseases following the necessary procedures to ensure it is non-hazardous and safe.
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    Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus
    Özkale, E; Dogan, O; Budak, M; Korkmaz, EM
    Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.
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    Cold pressed Pinus halepensis Mill. seed oil for potential health applications: Analgesic, anti-inflammatory effects, and assessment of inflammatory mediators by RT-qPCR in skin wound healing
    Atmane, SA; Batir, MB; Özbek, ZA; Ergönül, PG; Balcan, E; Eldjoudi, DA; Özkale, E; Bribi, N; Khettal, B
    Ethnopharmacological relevance: Pinus halepensis Mill. seed (Pinaceae), commonly known as Zgougou, is widely consumed in the Mediterranean region and has long been used to treat diseases including bronchitis, rheumatism, infection, and inflammation.Aim of the study: The present study was focused on the investigation of some pharmacological activities, such as analgesic, anti-inflammatory, and wound healing effects, of cold-pressed oil of Pinus halepensis Mill. seed (COPHS).Materials and methods: The fixed oil of Pinus halepensis seed was extracted by a cold pressing process. The analgesic activity of COPHS was examined by acetic acid and formalin-induced contortion and pain tests. The anti-inflammatory effects were evaluated in carrageenan and formalin induced paw and ear edema models. Wound healing potential was assessed on an experimental skin wound, and the expression levels of inflammation mediators were determined by RT-qPCR in skin wound healing. Results: The results showed analgesic efficacy through significant inhibition of abdominal cramps (59.15%) and pain (75.91%). In addition, this oil exerted an anti-inflammatory effect by inhibiting ear (62.25%) and paw (70.00%) edema. The COPHS stimulated wound contraction in experimental skin wound healing with a contraction rate of 89.23% with notable reduction of TNF-alpha and NF-kB expression levels in the treated groups. Conclusions: This study provided for the first time the pharmacological profile, particularly the analgesic, antiinflammatory, and healing effects, of fixed oil extracted by cold pressing from the seed of Pinus halepensis Mill.