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Öğe Potential stress tolerance roles of barley germins and GLPs(Springer, 2021) Karlık, ElifGermins and germin-like proteins (GLPs) known as germination markers are encoded by multigene families in several plant species, including barley. To date, functional analysis has revealed germins and GLPs are involved in diverse processes such as embryonic development and stress responses. The aim of this study was the analysis of barley germins and GLPs. In this study, 80 putative germins and GLPs have been identified in barley by using known 17 germins and GLP sequences. Analysis of germins and GLPs showed all germins and GLPs are distributed on all seven chromosomes that most of them spread through chromosome 3, 4 and 7 with 16, 18 and 12 proteins on each, respectively. The protein sizes varied between 185 and 335 amino acids, with an average length of 225 aa. Twelve conserved motifs were found. While germin motifs 1 and 3 were detected in all germins and GLPs, some motifs were found to be related to signalization. Interestingly, protein-protein interaction analysis demonstrated some GLPs are associated with RAB6-interacting golgin, oligopeptide transmembrane transporter activity, beta-glucuronidase activity, protein N-linked glycosylation, multi-pass membrane protein, and proteins containing zinc finger (Znf) domain and RING (really interesting new gene)-type zinc finger domains. Our findings suggest that barley germins and GLPs may have diverse functions that make them important candidates for crop improvement.Öğe Display of Sukkula distributions on barley roots via in situ hybridization(Firenze University Press, 2020) Karlık, ElifRetrotransposon are an abundant and ancient parts of the plant genomes that especially LTR retrotransposons influence the genome size and evolution. Sukku-la is a non-autonomous and active, relatively high copy-number retroelement. In this study, we performed fluorescence in situ hybridization (FISH) to observe the distributions of Sukkula elements (LTRs and internal-domain) by using labelled-PCR products. The localizations of Sukkula elements (LTRs and internal-domain) were observed under confocal microscope on Hordeum vulgare L. cv. Hasat root preparations. Our results revealed that Sukkula elements is still active and spread through the whole barley chro-mosomes. Additionally, the re-sequencing analysis of Sukkula LTRs demonstrated that LTRs sequences had ~65 bp gain. These analyses represent a valuable resource to reveal genome organization of barley and large sized plants.Öğe Endogenous retrovirus HERV-K6 and HERV-K11 polymorphisms’ analyses in head and neck squamous cell carcinoma patients(Elsevier B.V., 2021) Karlık, Elif; Gürbüz, Orkun; Yıldız, Yemliha; Gözükırmızı, NerminMany tumors, such as melanoma, breast cancer, germ cell tumors, renal cancer or ovarian cancer, express HERV proteins, mainly HERV-K (HML6) and HERV-K (HML2). However, there is no report showing any relation between squamous cell carcinoma of head and neck (HNSCC) and HERVs in literature. Here we report the polymorphic changes of HERV-K6 and HERV-K11 in tumor tissue samples of HNSCC patients comparing with healthy individuals. For this purpose, genomic DNAs from tumor tissue samples of 2 healthy individuals and of 8 HNSCC patients were isolated and IRAP-PCR was performed. IRAP-PCR analyses demonstrated that there were 18–73% polymorphism rates for HERV-K6 and 38–100% polymorphism rates for HERV-K11 among all the samples. There were also polymorphic changes between two control materials. Therefore, HERV-K6 polymorphisms may arise on an individual-specific basis. In the previous studies, some associations have been reported between the expression of HERVs and some cancer types or other major diseases. However, few reports have analyzed HERV-K movements among HNSCC patients. This report is the first study investigating HERV-K6 and HERV-K11 retrotransposon polymorphic changes in HNSCC patients.Öğe Transposon studies on colchium chalcedonicum(DergiPark, 2019) Karlık, Elif; Albayrak, Merve; Üzen, Erdal; Gözükırmızı, NerminColchicum chalcedonicum is one of the endemic plants in Turkey. The aim of this study was the investigation of the retrotransposon SIRE1, Sukkula and Nikita presence and insertion patterns in C. chalcedonicum. The plant samples were collected from the botanic garden of the Istanbul University. DNA isolation was performed from leaves by using modified CTAB/SEVAG protocol. Retrotransposon movements were investigated using SIRE1, Sukkula and Nikita primers by Inter Retrotranposon Amplified Polymorphism PCR technique (IRAP-PCR). Polymorphism percentages (%) were calculated based on Jaccard Similarity Index. We observed that polymorphism ratios of SIRE1, Sukkula and Nikita retrotransposons among all samples were 0-40%, 0- 100% and 0-60%, respectively. This is the first report to demonstrate three barley ? SIRE1, Sukkula and Nikita? retrotransposons presence and movements in C. chalcedonicum which is belonged to Colchium family, thus these IRAP primers may be used in further characterization and diversity studies of Colchicum family.Öğe Distinctive SIRE1 retrotransposon patterns on barley chromosomes(DergiPark, 2021) Karlık, Elif; Gözükırmızı, NerminSIRE1 is an active and relatively high copy-number retroelement belongs to the Tyl/Copia long terminal repeat (LTR) retrotransposon superfamily. Distinctive SIRE1 elements (ENV and GAG) distributions in barley genome were observed by using fluorescent in situ hybridization (FISH). We performed PCR to obtain tetramethylrhodamine-dUTP (TRITC)-labelled probes. Localizations of SIRE1 ENV and GAG domains were demonstrated under confocal microscope on Hordeum vulgare L. cv. Hasat root preparations. Our results revealed the distributions of SIRE1 elements ENV and GAG in barley genome. These results may provide to uncover the organization of SIRE retrotransposon pattern in barley genome.Öğe Pioneering in vitro studies for callus formation of colchicum chalcedonicum azn.(TRAKYA UNIV BALKAN YERLESESI ENSTITULER BINASI, 2020) Karlık, Elif; Değer, Meltem; Üzen, Erdal; Gözükırmızı, NerminColchicum calcedonicum Azn is one of the endemic species distributed in Turkey, where many endemic plant species occur. It has long-oval shaped corm under the soil, and usually 3-4 leaves on it. In vitro production of endemic species using callus culture has become promising study for conservation. The aim of this study is to generate an efficient callus protocol for in vitro production of C. chalcedonicum. To sterilize the explants, 0.25% (w/v) mercuric chloride (HgCl2) was used for 20 min. In addition to mercuric chloride, surface sterilization was conducted by using 6.5% NaCl with Tween 80 for 30 min. We used 19 different mediums and the primary callus formation was obtained in Murashige & Skoog's basal medium (MS) supplemented with 2,4-D (2 mg L-1), 2IP (0.5 mg L-1), 3% sucrose and 0.05% active carbon. Our study demonstrated the active carbon usage was effective for the primary callus formation. This study is the first report for primary callus formation of C. chalcedonicum. However, our work is a pioneering study to improve callus formation protocol system for in vitro conservation of endemic species C. chalcedonicum.Öğe Comparison of local anesthetic efficiency of tramadol hydrochloride and lidocaine hydrochloride(W B Saunders Co-Elsevier Inc, 2018) Ege, Bilal; Çalışır, Metin; Al-Haideri, Yahya; Ege, Miray; Güngörmüş, MetinPurpose: This study investigated the local anesthetic efficiency of tramadol versus lidocaine hydrochloride in maxillary infiltration anesthesia. Materials and Methods: This study was a randomized double-blinded study involving 50 healthy volunteers. In the experimental part of this study, each volunteer received a buccal 0.5-mL injection of tramadol hydrochloride 25 mg on one side and a buccal 0.5-mL injection of vasoconstrictor-free lidocaine hydrochloride 20 mg on the other side. No other treatment was performed. After the injections, total duration of anesthesia, start and finish times of anesthesia, soft tissue (sensory) innervation, depth of anesthetic, possible side effects, and satisfaction levels were recorded from all volunteers. Results: There was no relevant difference between solutions for total anesthesia duration and peak values. However, statistically, the effect of lidocaine started and ended early. The efficacy of tramadol was markedly more effective in the gingiva and skin, especially at 15 and 20 minutes, compared with lidocaine. Both anesthetic agents were well tolerated by the volunteers. Conclusion: Tramadol hydrochloride can be a good alternative to local anesthetic agents and beneficial to support anesthesia during long operations. (C) 2017 American Association of Oral and Maxillofacial Surgeons.Öğe Expression analysis of lncRNA AK370814 involved in the barley vitamin B6 salvage pathway under salinity(Springer, 2018) Karlık, Elif; Gözükırmızı, NerminLong non-coding RNAs (lncRNAs), which are longer than > 200 nt, perform various functions in a variety of important biological processes. The aim of this study is the investigation of relative expression levels of AK372815 putative pyridoxal reductase (PLR) gene and sense lncRNA AK370814 on four barley genotypes (Hasat, Beysehir 99, Konevi 98 and Tarm 92) in response to 150 mM salinity application during 3 days post-germination. Seeds were placed randomly in petri dishes containing (a) only H2O (control), (b) 150 mM NaCl, for 72 h. RNA isolation was carried out using TriPureA (R) reagent from 150 mM salt-treated root and shoot samples. Relative expression levels of AK372815 PLR and sense lncRNA AK370814 were determined by qPCR. Results demonstrated that salinity affected the expression levels of both AK372815 PLR gene and sense lncRNA AK370814 during germination. Although expression levels of AK372815 PLR tended to be down-regulated under salinity, expression levels of sense lncRNA AK370814 were up-regulated. Another goal of this study is improvement of alternative approach to NGS technologies for determination of relative expression levels of sense lncRNAs under particular circumstances. This is the first report that demonstrates a relationship between lncRNA and vitamin B6 salvage pathway.Öğe LncRNAs: genetic and epigenetic effects in plants(Taylor & Francis Ltd, 2019)Long non-coding RNAs (lncRNAs) transcribed from the eukaryotic genome play important roles in essential biological processes, transcriptional and post-transcriptional gene regulation. LncRNAs act both in the nucleus and in the cytoplasm, mostly in association with chromatin in the nucleus. LncRNAs appear to be important regulators of gene expression, gene regulation and genome stability. This review outlines the major types of plant lncRNAs, their genetic and epigenetic effects with a focus on plant lncRNA instances, and discusses the recent advances in our understanding of their mechanism of action.Öğe New gene expression regulators: long non-coding RNAs(Amer Inst Physics, 2019) Gözükırmızı, Nermin; Karlık, ElifLong non-coding RNAs (lncRNAs) play key roles in the regulation of biological processes including response to environmental stresses either transcriptional or post-transcriptional levels. The salinity tolerance of barley may play an important role in understanding the salinity mechanism. The aim of this study is the investigation of molecular responses of four barley genotypes Hordeum vulgare L. (Hasat, Beysehir 99, Konevi 98 and Tarm 92) to 150 mM salinity during 3 days of germination period. To reveal the effect of lncRNAs, we performed Real-time PCR and fluorescence in situ hybridization (FISH) studies. Study demonstrated salinity affected the expression levels of four lncRNAs, CNT0018772, CNT0031477, AK363461, and AK370506, during germination. Previous studies have shown that there was no statistical difference between barley varieties for expression level of CNT0018772 (p>0.05). However, our study indicated that there was statistically significant difference between barley varieties for CNT0031477 (p<0.05). Additionally, there was statistically significant difference between barley varieties for the two barley lncRNAs of AK363461 and AK370506, (p<0.05). We were also able to observe the localization of these four lncRNAs on barley chromosomes, which were exhibited under confocal microscope via in situ hybridization on barley root preparations. This study further supports the reasons why nowadays, lncRNAs are considered as major regulators.Öğe Genome organization changes in GM and non-GM soybean [Glycine max(L.) Merr.] under salinity stress by retro-transposition events(Springer, 2020) Şahin, Olcay; Karlık, Elif; Meriç, Sinan; Arı, Şule; Gözükırmızı, NerminGenetically modified (GM) crops are developed and cultivated worldwide, providing protection against insects and diseases, or tolerance to herbicides. However, despite the advantages that GM crops, they pose many concerns not only to human and animal health but also to the environment. In the present study, we perform inter-retrotransposon amplified polymorphism (IRAP)-PCR to revealSIRE1,Bagy2andNikitatransposition events in soybean [Glycine max(L.) Merr.] and GM soybean under increasing salt stress conditions (0 mM as control, 80 mm, 120 mM, 160 mM and 200 mM NaCl). Salinity dramatically affected soybean and GM soybean in a similar way that stem lengths, root lengths and leaf areas were reduced compared to control. According to IRAP-PCR results, polymorphism ratios ofSIRE1,Bagy2andNikitaretrotransposons among all samples were found to be 22-100%, 0-73% and 37-100%, respectively. These results are the first direct report to demonstrate the relationship between TEs polymorphisms and salinity stress in soybean and GM soybean. TEs, which may explain part of the new phenotypes, play essential roles in genome and gene evolution. Such information can be useful to understanding of genome organization differences derived from TEs between soybean and GM soybean.
