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Öğe Bacteria isolated from Triticum monococcum ssp. monococcum roots can improve wheat hologenome in agriculture(Springer, 2022) Ünüvar, Ömer Can; Zencirci, Nusret; Ünlü, Ercan SelçukBackground Triticum monococcum ssp. monococcum is an ancestral wheat species originated from Karacadag Mountain of Turkey more than ten thousand years ago. Because of environmental and anthropogenic effects, food supply and demand are not balanced. Agricultural activities such as breeding, and fertilization are important to sustain the balance. Conventional breeding and fertilization applications usually neglect contribution of plant related hologenomes in agricultural yield. The disruption of plant growth promoting microorganisms results in intensive usage of chemical fertilizers. The harmony between plant and plant-associated microorganisms is important for sustainability. In this study, isolation, biochemical characterization, and impact on plant growth parameters of natural bacteria associated with Triticum monococcum ssp. monococcum hologenome were aimed. Methods and results The collection of root samples and isolations of the root-associated bacterial species were carried out from local wheat lands. According to interpretation of three identification methods (MALDI-TOF, 16S rDNA, 16S-23S rDNA) eight isolates are Arthrobacter spp. ESU164, Arthrobacter spp. ESU193, Pseudomonas spp. ESU131, Pseudomonas spp. ESU141, Pseudomonas poae strain ESU182, Pseudomonas thivervalensis strain ESU192, Pseudomonas spp. ESU1531, Bacillus subtilis strain ESU181. For each isolate we investigated biochemical properties especially nitrogen fixation, phosphate solubilization, and indole-3-acetic acid production abilities. The results show that all isolates are nitrogen fixers and the best phosphate solubilizer have been reported as Pseudomonas spp. ESU131 with 2.805 +/- 0.439. Conclusions All isolates are indole-3-acetic acid productors. 2 isolates affected the coleoptile lengths, 7 bacterial isolates showed statistically positive effect on root number, and 5 isolates promote the root lengths and the root fresh weights.Öğe Caulerpa racemosa (Terörist Yosun) Tu?ru?ne Ait Alternatif Oksidazların Tanımlanması ve Karakterizasyonu(2017) Ünlü, Ercan SelçukAlternatif oksidazlar bitkilerde, funguslarda ve alglerde tanımlanmıstır. AOX proteinlerinin islevi elektron transport zinciri boyunca elektron akısı ve mitokondriyal retrograd sinyal yolagı için tanımlanmıstır. AOX proteinlerinin görevleri eseyli ve eseysiz u?reme, biyotik ve abiyotik stres çesitlerine karsı direnç mekanizmalarında yer alır. Caulerpa cylindracea istilacı bir deniz algidir. Istilanın etkileri Akdeniz?den Ege kıyılarına kadar gözlenmistir. C. cylindracea tu?ru? diger tu?rlere göre soguk, açlık, patojen saldırısı gibi stres kosullarına karsı gösterdikleri direnç ve u?reme kapasiteleri ile u?stu?nlu?k saglamaktadır. Ek olarak C. cylindracea çözu?nmu?s oksijen seviyesini azaltarak, zemin kimyasal özelliklerini degistirerek ve de ikincil metabolit u?retim yoluyla zararlı etkilere sebep olmaktadır. C. cylindracea?nın nis u?zerinde avantajlarını ve alternatif oksidaz proteinlerinin tanımlanmıs islevsel rollerini karsılastırdıgımızda, AOX proteinlerinin C. cylindracea?da bu avantajlı özellikleri gelistirmelerinde etkili oldukları muhtemeldir. Bununla birlikte, önceki arastırmalar genellikle fenotipik yaklasımları kullanarak tu?rlerin karakterizasyonu u?zerine odaklanmıstır. Tu?ru?n stres direnci ve istilacı özelliklerine katkı saglayan biyokimyasal ve moleku?ler mekanizmalar hakkında sınırlı veri bulunmaktadır. Bu projenin amacı, C. cylindracea tu?ru?ne ait alternatif oksidazları tanımlamak ve karakterize etmektir. Bu dogrultuda Seferihisar / Izmir'den örnekler toplandı ve transkriptom analizi gerçeklestirildi. Birlestirilmis RNA-Seq verilerinden 47400 transkript tanımlanmıstır. Ayrıntılı biyoinformatik analiz sonucunda mitokondriyal alternatif oksidaz proteinlerini kodlayan iki gen tanımlanmıstır. S. cerevisiae içinde AOX proteinlerinin ekspresyonu, AOX gen dizilerinde S. cerevisiae genomu için nadir bulunan kodonların varlıgından dolayı basarılı olmamıstır. Ayrıca, iki proteinin yapısal organizasyonu biyoinformatik yöntemlerle incelenmistir. Proteinlerin her ikisi de karakteristik demir baglama alanlarını tasımakta ve tersiyer yapıları diger bitki AOX proteinleri için tarif edildigi gibi karakteristik heliks organizasyonunu göstermektedir.Öğe Characterization of fungal RTG2 genes in retrograde signaling of Saccharomyces cerevisiae(2013) Ünlü, Ercan Selçuk; Narayanan, Lakshmi; Gordon, Donna M.Changes in the functional status of mitochondria result in the transcriptional activation of a subset of nuclear-encoded genes in a process referred to as retrograde signaling. In Saccharomyces cerevisiae, this molecular link between mitochondria and the nuclear genome is controlled by three key signaling proteins: Rtg1p, Rtg2p, and Rtg3p. Although the retrograde signaling response has been well characterized in S. cerevisiae, very little is known about this pathway in other fungi. In this study, we selected four species having uncharacterized open reading frames (ORFs) with more than 66% amino acid identity to Rtg2p for further analysis. To determine whether these putative RTG2 ORFs encoded bona fide regulators of retrograde signaling, we tested their ability to complement the defects associated with the S. cerevisiae rtg2? mutant. Specifically, we tested for complementation of citrate synthase (CIT2) and aconitase (ACO1) at the transcript and protein levels, glutamate auxotrophy, and changes in the interaction between Rtg2p and the negative regulator Mks1p. Our findings show that all four Rtg2p homologs are functional upon activation of retrograde signaling, although their degree of complementation varied. In addition, all Rtg2p homologs showed a marked reduction in Mks1p binding, which may contribute to their altered responses to retrograde signaling. © 2013 The Authors.Öğe A combined de novo assembly approach increases the quality of prokaryotic draft genomes(Springer, 2022) Çabuk, Uğur; Ünlü, Ercan SelçukNext-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.Öğe Comparative de novo transcriptome analysis and random UV mutagenesis: Application in high biomass and astaxanthin production enhancement for Haematococcus pluvialis(Springer, 2023) Telli, Murat; Ünlü, Ercan SelçukBackgroundAstaxanthin is a natural carotenoid with strong antioxidant capacity. The high demand on astaxanthin by cosmetic, food, pharmaceutical and aquaculture industries promote its value in the biotechnological research. Haematococcus pluvialis Flotow 1844 has been characterized as one of the most promising species for natural astaxanthin biosynthesis. Even though H. pluvialis as an advantage in producing astaxanthin, its slow grow-yield limits usage of the species for large-scale production.Methods and ResultsIn this study we generated mutated H. pluvialis strain by using one-step random UV mutagenesis approach for higher biomass production in the green flagellated period and in turn higher astaxanthin accumulation in red stage per unit algae harvest. Isolated mutant strains were tested for the astaxanthin accumulation and yield of biomass. Among tested strains only mutant strain designated as only MT-3-7-2 showed a consistent and higher growth pattern, the rest had shown a fluctuated and then decreased growth rate than wild type. To demonstrate the phenotypical changes in MT-3-7-2 is associated with transcriptome, we carried out comparative analysis of transcriptome profiles between MT-3-7-2 and the wild type strains. De novo assembly was carried out to obtain the transcripts. Differential expression levels for the transcripts were evaluated by functional annotation analysis.ConclusionsData showed that increased biomass for the MT-3-7-2 strain was different from wild type with expression of transcripts upregulated in carbohydrate metabolism and downregulated in lipid metabolisms. Our data suggests a switching mechanism is enrolled between carbohydrate and lipid metabolism to regulate cell proliferation and stress responses.Öğe Dielectric properties of porcine skin tissue and in vivo testing of implantable antennas using pigs as model animals(IEEE, 2012) Karaçolak, Tutku; Cooper, Robert; Ünlü, Ercan Selçuk; Topsakal, ErdemThe development of most medical systems depends on the accurate characterization of the dielectric properties [relative permittivity (epsilon(r))and conductivity (sigma)] of biological tissues. The main objective of this study is to measure the dielectric properties of porcine skin tissue in the frequency range of 300 MHz-3 GHz. The skin samples were provided from three pigs of same age, sex, and breed. The measured data was similar to the dielectric properties of human skin tissue. A three-pole Cole-Cole model is also used to fit the dielectric properties as a function of frequency for future studies. To show porcine skin tissue may be used as a substitute for human skin, implantable antennas designed using human-skin electrical properties are fabricated. The antennas are surgically implanted into two porcine test subjects at the Mississippi State University (MSU) College of Veterinary Medicine, and return loss measurements are carried out. In vivo studies are performed over the course of two weeks to verify the proper vaibility of the antennas. Antenna measurements show that porcine and human skin tissues give similar responses.Öğe Effects of moderate high temperature and UV-B on accumulation of withanolides and relative expression of the squalene synthase gene in Physalis peruviana(Tubitak Scientific & Technical Research Council Turkey, 2020) Şahin, Günce; Telli, Murat; Ünlü, Ercan Selçuk; Pehlivan Karakaş, FatmaPhysalis peruviana L. (Cape gooseberry) is a source for a variety of phytocompounds such as withanolides, withanone, withaferin A, and withanolide A. These withanolides are high-value drug candidates due to their various pharmacological properties. To meet the increasing demands for these compounds, plant cell technology offers a reliable alternative. Exogenous addition of elicitors is considered the most effective strategy for enhanced production of secondary metabolites. In this study, we investigated changes in withanolide accumulation and characterized the gene expression level changes of squalene synthase enzyme in P. peruviana shoot cultures exposed to mild nonlethal heat stress (45 degrees C for 2 and 5 h) and UV-B radiation (313 nm for 15 min and 3 h). We demonstrated significant changes in withanolide content with 7.86- and 12.5-fold increases for 2- and 5-hmild high-temperature exposure times, respectively. Exposure to UV-B also changed the withanolide content by 7.22- and 7-fold increases for 15 min and 3 h exposure times, respectively. The relative expression level of squalene synthase gene showed consistent results with1.80- and 10.13-fold increases in withanolide for 2- and 5-h mild high-temperature exposure times, and 1.34- and 2.01-fold increases with 15 min and 3 h UV-B exposure times, respectively.Öğe From Hologenomes to Biofertilizers in Wheat Production(Springer International Publishing, 2022) Ünüvar, Ömer Can; Ünlü, Ercan SelçukBiofertilizers are defined as the liquid or solid mixtures containing living microorganism(s) specifically produced to promote plant growth and increase crop yield in agricultural practices. They are one of the most promising alternatives for maintaining a sustainable environment in agriculture. Several studies show the benefits of microorganism(s) in crop yield. The concept is directly related with the hologenome assembly of the plants. Usage of chemical fertilizers not only disrupts the assemblies but also adversely affects the soil quality. Several published studies show that supporting especially wheat roots through the plant growth-promoting bacteria (PGPB) would enhance plants’ availability for nitrogen, phosphorus, zinc, siderophores, and auxin hormones. While PGPB enhance the nutritional status of the plants, they also provide additional defense against various biotic and abiotic stress conditions. Hologenome is a term used to describe the net genetic information of the plant host and associated microbiota. From ancient wheat to modern cultivar, the core hologenome assemblies preserved even the human influences on the species. The conservation of the assemblies also suggests that the survival of wheat species extremely depended on the associated microorganisms. Data suggests that the incorporation of biofertilizers developed by considering the associated hologenomes of ancient wheat species would not only be beneficial for increasing the yield and quality in agricultural production of wheat but also for the ecology itself. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022.Öğe Identification and expressional profiling of putative MAX1 gene in sugar beet (Beta Vulgaris L.)(2020) Ünlü, Ercan Selçuk; Gürel, Songül; Aflaki, Fatemeh; Pazuki, Arman; Şahin, Günce; Gürel, EkremSugar beet is an industrial crop cultivated mostly for sucrose production. Today, modern hybridization applications have raised the sugar content to 20%. Considering the increased demand globally, it is required to develop new yield–increasing application strategies. This requires extensive knowledge of the genetic mechanisms to control plant growth and metabolism. Investigation of phytohormones is promising to increase our knowledge of plant growth and developmental processes. Strigolactones are recently introduced plant hormones. They are responsible for shoot and root architecture, and involved in development, communication, germination, and responses to stress. Four major proteins (AtD27, MAX1, MAX3, MAX4) are responsible for the strigolactone biosynthesis. MAX1 protein is essential for the distinct production of strigolactone molecules. The studies on strigolactones have been carried out mostly using Arabidopsis thaliana. There are only few studies on agriculturally important plants. No reports are available for the investigation of strigolactone biosynthesis in sugar beet (Beta vulgaris). In this manuscript, we profiled the expression of MAX1 gene in sugar beet treated with strigolactone hormones (rac-GR24, (±)-strigol and (±)-5-deoxystrigol) and a strigolactone biosynthesis inhibitor (TIS108). Our data suggest that MAX1 has a conserved biosynthetic and regulatory metabolism in sugar beet compared to previously investigated plant species.Öğe Identification of alternative oxidase encoding genes in Caulerpa cylindracea by de novo RNA-Seq assembly analysis(Elsevier, 2019) Ünlü, Ercan Selçuk; Ünüvar, Ömer Can; Aydın, MeryemAlternative oxidases (AOX) are defined in plants, fungi and algae. The main function of AOX proteins has been described for electron flow through electron transport chain and regulation of mitochondrial retrograde signaling pathway. The roles of AOX proteins have been characterized in reproduction and resistance against oxidative stress, cold stress, starvation, and biotic attacks. Caulerpa cylindracea is an invasive marine green alga. Although the natural habitats of the species are Australia coasts, the impact of the invasion has been monitored through the Mediterranean Sea and the Aegean Sea. C. cylindracea species have advantages against others by showing higher resistance to stress conditions such as cold, starvation, pathogen attacks and by their capability of sexual and vegetative reproduction. Comparing the advantages of C. cylindracea over the niche and defined functional roles of mitochondrial AOX proteins, it is evident that AOX proteins are likely involved in developing those advantageous skills in C. cylindracea. However, there is limited data about biochemical and molecular mechanisms that take part in stress resistance and Invasion characteristics. We aimed to identify mitochondrial alternative oxidase encoding genes in C. cylindracea while annotating whole transcriptome data for the species. Samples were collected from Seferihisailizmir. Transcriptome analysis from pooled RNA samples revealed 47,400 assembled contigs represented by 33,340 unigenes. Using standalone Blast analysis, we were able to identify two alternative oxidase encoding genes.Öğe Identification of conserved microRNA molecules in einkorn wheat (Triticum monococcum spp. monococcum) by deep sequencing analysis(Wiley-Blackwell, 2016) Ünlü, Ercan Selçuk; Bataw, Sara; Kaya, Özge; Zencirci, NusretGlucocorticoid receptor (GR) is one of the involved receptors and its gene has been recognized as a candidate gene for major depressive disorder and bipolar disorder. The involvement of the GR gene (NR3C1) locus on human chromosome 5q31-q32. The N363S (rs6195) is located within exon 2 and changes the second base of codon 363, leading to asparagine to serine substitution in the transactivation domain of GR. In this study, we aimed to examine the role of NR3C1 N363S polymorphisms in genetic susceptibility to MDD development in a Turkish population. A total of 100 consecutive unrelated adult patients with documented medical records of MDD were from outpatient Psychiatry Clinic in Gaziosmanpasa University Research and Training Hospital, Tokat, Turkey by referral from the treating physician, after obtaining initial verbal consent to participate in the study. In addition, 100 control subjects from the same area as the patients, and comprising blood donors, healthy volunteers were enrolled this study. DNA was isolated from peripheral blood samples and the N363S variant was screened by the RT-PCR technique. 99 out of the 100 MDD patients were found to be AA genotype at the N363S (AA genotype frequency 0.99; A-allele frequency 0.995). Also, 1 out of the 100 MDD patients was found to be AG genotype (AG genotype frequency 0.01; G-allele frequency 0.005). No homozygote for the rare G-allele was seen. Significantly more frequent occurrence of allele-A in N363S polymorphism was observed in the group of the patients with MDD in comparison with the control group (OR: 4.061, 95% CI: 0.449–36.660, v2 : 1.823, p: 0.177). For genotype AG versus AA, no significant correlation was demonstrated between patients and the control group with respect to the investigated SNP (OR: 0.242, 95% CI: 0.027–2.208, v2 : 1.846, p: 0.1742). This study was supported by the Gaziosmanpas a University Scientific Research Fund (GOU BAP2013/8).Öğe Identification of conserved miRNA molecules in einkorn Wheat (Triticum Monococcum subsp. Monococcum) by using small RNA sequencing analysis(2018) Ünlü, Ercan Selçuk; Bataw, Sara; Şen, Didem Aslan; Şahin, Yunus; Zencirci, NusretTriticum monococcum subsp. monococcum as a first cultivated diploid wheat species possesses desirable agronomic and quality characteristics. Drought and salinity are the most dramatic environmental stress factors that have serious impact on yield and quality of crops; however, plants can use alternative defense mechanisms against these stresses. The posttranscriptional alteration of gene expression by microRNAs (miRNAs) is one of the most conserved mechanisms. In plant species including wheat genomes, miRNAs have been implicated in the management of salt and drought stress; however, studies on einkorn wheat (Triticum monococcum subsp. monococcum) are not yet available. In this study, we aimed to identify conserved miRNAs in einkorn wheat using next generation sequencing technology and bioinformatics analysis. In order to include a larger set of miRNAs, small RNA molecules from pooled plant samples grown under normal, drought, and salinity conditions were used for the library preparation and sequence analysis. After bioinformatics analysis, we identified 167 putative mature miRNA sequences belonging to 140 distinct miRNA families. We also presented a comparative analysis to propose that miRNAs and their target genes were involved in salt and drought stress control in addition to a comprehensive analysis of the scanned target genes in the T. aestivum genome.Öğe Meta-analysis of sugar beet (Beta vulgaris L.) transcriptome profiles under different biotic and abiotic stress conditions(Springer, 2023) Bulut, Burak; Gürel, Songül; Ünüvar, Ömer Can; Gürel, Ekrem; Ünlü, Ercan SelçukSugar beet (Beta vulgaris L.) meets the 21% of world sugar production. Soil pollution, biotic and abiotic factors in production areas greatly reduce product quantity and quality. Sugar beet responds to biotic and abiotic stresses such as drought, salt, heat, light, and infections of nematode, bacteria and fungi at the molecular level. Understanding molecular mechanisms require comprehensive genomics studies in order to control these mechanisms to increase the yield and quality. Transcriptome studies performed under stress conditions can shed light on the responses of plants at the molecular level. In addition, meta-analysis can help to find common responses under different stress conditions. In this study four different stress-related transcriptome data were used: two of them are related with biotic stress (nematode and fungi infection) and two of them are related with abiotic stress (ABA treatment and salt stress). In this study, we performed meta-analysis of studies conducted under biotic and abiotic stress conditions. Our results revealed 460 commonly regulated genes from biotic stress related data and 1031 commonly regulated genes from abiotic stress related data. Our data also showed that expression of ten genes is controlled regardless of the type of stress condition. The data can be useful for understanding the molecular aspect of adaptive stress response in sugar beet.Öğe De novo assembly and annotation of microalga tetradesmus obliquus transcriptome(Central Fisheries Research Institute, 2022) Ünüvar, Ömer Can; Ünlü, Ercan SelçukTetradesmus obliquus is a unicellular green microalga and considered as a potential source for biotechnological production of pigments such as lutein. No genome-related data is available for T. obliquus that would increase the ability to develop new approaches in biotechnological applications. We present the first transcriptome data for T. obliquus. The aim of this study is to provide a comprehensive transcriptome annotation and identification of conserved genes involved in lutein pigment biosynthesis in Tetradesmus obliquus cells by analyzing pooled RNA-Seq data. Next-Generation Sequencing was applied for the pooled cDNAs library prepared by combining the cell cultures collected from samples exposed to dark and high light intensity conditions. Transcripts were assembled by the de novo assembly approach. Trinotate software was used for functional annotation of assembled transcripts. We also carried out BLAST analysis comparing the transcriptome data against known lutein biosynthesis genes. The 49.15% of the assembled sequences were functionally annotated, providing a total of 21490 unigenes. Our data also revealed the transcript sequences for ten conserved genes required for lutein biosynthesis. The data produced in this study can be used for molecular approaches in biotechnological applications related to T. obliquus, such as increasing the yield of pigment production.Öğe Şeker Pancarında (Beta vulgaris) Sitokrom P450'yi Kodlayan Genin Ekspresyon Düzeyinin Strigolakton Biyosentez Süreci ile İlişkisinin Karakterizasyonu ve Strigolaktonların Fizyolojik Etkilerinin Belirlenmesi(2019) Gürel, Songül; Gürel, Ekrem; Şahin, Günce; Ünlü, Ercan SelçukKarotenoidlerden kökenlenen ve yeni nesil hormonlar olarak bilinen strigolaktonlar (SL), kök ve gövde olusumunu düzenleyici, kök paraziti bitkilerin çimlenmesini uyarıcı, besin stresine karsı kök ve gövde olusumunu düzenleyici, metabolik ve çevresel uyarıcılara tepki ve savunma mekanizmalarında etkili ve sekonder büyümeyi tesvik eden bitki büyüme düzenleyicileridir. MAX1 geninin SL'ların biyosentezindeki veya sinyallemesindeki rollerini degerlendirmek ve seker pancarında (Beta vulgaris L.) ilk kez sorumlu geni tanımlamak için yapılan çalısmalarda SL'ların (rac-GR24, strigol ve 5-deoksistrigol) ve SL inhibitörünün (TIS108) farklı konsantrasyonlarda (0.0, 2.5, 5.0 ve 7.5 ?M) seker pancarında sitokrom P450 711A1 ekspresyonu üzerine etkisi incelenmistir. Elde edilen sonuçlara göre SL'ların eksojen uygulaması gen ifadesini azaltmıs ve SL inhibitörü ise genin ifadesini arttırmıstır. Tuzluluk ve kuraklık gibi stres kosullarına SL'ların etkilerinin belirlenmesi amacıyla yapılan denemelerde, hormon uygulamaları Chl a ve toplam Chl miktarını önemli ölçüde artırırken Chl b miktarındaki artıs önemli olmamıstır. Bununla birlikte, strese maruz kalan bitkilerde CAT enzim aktivitesi üzerindeki hormonal uygulamanın etkileri istatistiksel olarak anlamlı olmamıstır. SL uygulamaları bitkilerde MDA miktarını azaltmıstır. SL'ların oksin ile etkilesimlerini in vitro kosullarda incelemek için besin ortamına çesitli konsantrasyonlarda SL ve oksin (rac-GR24 ve IAA) veya SL ve oksin inhibitörleri (TIS108 ve TIBA) yedi farklı kombinasyonda eklenmistir. En yüksek yaprak sayısı ve en uzun yaprak, kontrol, TIS108 ve TIS108+IAA uygulamalarında gözlenirken, TIBA içeren kombinasyonlarda yaprak sayısı azalmıs ve yaprak boyu kısalmıstır. En büyük yaprak alanı kontrol ve TIS108 uygulamaları için kaydedilmistir. Kontrol uygulamasında seker pancarı bitkileri en uzun kökleri olustururken, en kısa kökler TIBA içeren kombinasyonlarda elde edilmistir. SL'ların seker pancarının in vitro doku kültürü üzerindeki etkilerini belirlemek için 0.0, 2.5, 5.0 ve 7.5 ?M konsantrasyonlarında ortama eklenen SL?lar bitkilerde yaprak sayısı, yaprak ve kök uzunlugunu azaltmıs, bir SL inhibitörü olan TIS108 yaprak gelisimini etkilememis ancak kök uzunlugunu azaltmıstır. SL'ların seker pancarı tohumunun çimlenmesi üzerindeki etkileri istatistiksel olarak önemli olmamıstır.Öğe Sequencing, de novo assembly and annotation of digitalis ferruginea subsp. schischkinii transcriptome(Springer, 2021) Ünlü, Ercan Selçuk; Kaya, Özge; Eker, İsmail; Gürel, EkremThere is an increasing demand for elucidating the biosynthetic pathway of medicinal plants, which are capable of producing several metabolites with great potentials for industrial drug production. Digitalis species are important medicinal plants for the production of cardenolide compounds. Advancement on culture techniques is strictly related to our understanding of the genomic background of species. There are a limited number of genomic studies on Digitalis species. The goal of this study is to contribute to the genomic data of Digitalis ferruginea subsp. schischkinii by presenting transcriptome annotation. Digitalis ferruginea subsp. schischkinii has a limited distribution in Turkey and Transcaucasia, and has a high level of lanatoside C, an important cardenolide. In the study, we sequenced the cDNA library prepared from RNA pools of D. ferruginea subsp. schischkinii tissues treated with various stress conditions. Comprehensive bioinformatics approaches were used for de novo assembly and functional annotation of D. ferruginea subsp. schischkinii transcriptome sequence data along with TF families predictions and phylogenetic analysis. In the study, 58,369 unigenes were predicted and unigenes were annotated by analyzing the sequence data in the non-redundant (NR) protein database, the non-redundant nucleotide (NT) database, Gene Orthology (GO), EuKaryotic Orthologous Groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, and InterPro databases. This study is the first transcriptome data for D. ferruginea subsp. schischkinii.Öğe Small RNA sequencing based identification of MiRNAs in daphnia magna(Public Library Science, 2015) Ünlü, Ercan Selçuk; Gordon, Donna M.; Telli, MuratSmall RNA molecules are short, non-coding RNAs identified for their crucial role in post-transcriptional regulation. A well-studied example includes miRNAs (microRNAs) which have been identified in several model organisms including the freshwater flea and planktonic crustacean Daphnia. A model for epigenetic-based studies with an available genome database, the identification of miRNAs and their potential role in regulating Daphnia gene expression has only recently garnered interest. Computational-based work using Daphnia pulex, has indicated the existence of 45 miRNAs, 14 of which have been experimentally verified. To extend this study, we took a sequencing approach towards identifying miRNAs present in a small RNA library isolated from Daphnia magna. Using Perl codes designed for comparative genomic analysis, 815,699 reads were obtained from 4 million raw reads and run against a database file of known miRNA sequences. Using this approach, we have identified 205 putative mature miRNA sequences belonging to 188 distinct miRNA families. Data from this study provides critical information necessary to begin an investigation into a role for these transcripts in the epigenetic regulation of Daphnia magna.Öğe Transcriptional response and functional target analyses of miRNA and mRNA to planktivorous fish kairomone exposure in Daphnia magna(E Schweızerbartsche Verlagsbuchhandlung, 2021) Telli, Murat; Gordon, Donna M.; Ünlü, Ercan SelçukThe discovery of regulatory functions for microRNAs (miRNA) and recently described miRNA profiles for Daphnia (Brachiopoda, Cladocera) make it an ideal system to probe for epigenetic regulation of predator avoidance mechanisms in aquatic ecosystems. In this study we report that exposing D. magna to kairomone released by predatory fish from birth to the first reproduction resulted in the differential expression of the four miRNAs tested: miR-7, miR-34, miR-317, and miR-375. Normalized transcript levels for each miRNA were found to vary across the exposure period with no clear conserved pattern of expression despite functional target analyses by Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicating that predicted miRNA target genes are likely involved in related biological activities. Analysis of mRNA transcripts (Hsp70, Hsp90 (HSP = heat shock protein), actin, AKT-interacting protein (AKT), Glycogen synthase (GYS) and Insulin growth factor receptor (IGFR)) identified in the literature as kairomone-mediated genes, were also carried out. Similar to that obtained for miRNAs, the mRNA relative expression levels showed varying degrees of temporal regulation across the exposure time with the two heat shock transcripts exhibiting elevated levels at early and late time points of exposure while the AKT, GYS, and IGFR transcripts had a general decrease in relative expression during the first 96 hours. Differential mRNA expression data supports the conclusion that kairomone mediated response is regulated by cost of general biological processes and that of survival under long-term kairomone stress. These studies lay the foundation for future work aimed at linking miRNAs and their target transcripts to changes in the signaling events that govern Daphnia response to kairomone specific stress.Öğe Transcriptome sequencing based identification of alternative oxidase genes in white water-lily, Nymphaea alba(Wiley-Blackwell, 2016) Yıldız, Gülgez Gökçe; Ünüvar, Ömer Can; Kaya, Özge; Ünlü, Ercan Selçuk[No Abstract Available]
