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Öğe Analysis of mirna in plants by next generation sequencing technology(Centenary University, 2016) Eren, Abdil Hakan; İlhan, Emre; İnal, BehçetmiRNAs (microRNAs) find in the intron sites of the genes. miRNAs are produced from their gene region and non-coding RNAs. In plants, the production of miRNAs that consist of 21–24 nucleotides in length starts in nucleus and continues coordinately in cytoplasm. miRNAs help to protect the integrity of genome duo to define expression levels of genes related to development and stress in plant. In this way, miRNAs are considered to defend 30% of eukaryotic genomes. There are a few types of small RNAs such as miRNAs, siRNAs, phasiRNAs and NAT – siRNAs in plants. Various methods such as Northern Blotting, Flow cytometer, cloning, qRT – PCR, Microarray, sequencing and RNA-seq (transcriptome profiling) were developed to detect and discover functions of these small RNAs. Species and tissue specific miRNAs can be easily identified with this method called as miRNA-seq, one of the Next Generation Sequencing methods. In miRNA studies, the algorithms such as miRDeep-Seq, miRanalyzer, miRCat, miRExpress, miRTRAP can be used. This review summarizes about up to date applications of next generation seqeuncing technologies in miRNA-seq studies. © 2016, Centenary University. All rights reserved.Öğe Antioxidant capacity and phylogenetic analysis of twenty native grape cultivars in Siirt province, Turkey(2018) Fidan, Mehmet; Erez, Mehmet Emre; İnal, Behçet; Pınar, Süleyman Mesut; Altıntaş, SerdarThe quality of grape cultivars not only depends on the grape cultivar but also is influenced by the molecular concepts and agro-climatic factors. For this purpose, four different grape cultivars were collected from five different locations in Siirt province (Turkey). Totally twenty different grape cultivars were investigated. In the present study, the antioxidant activity (total phenolic, flavonoid, proanthocyanidin content, DPPH and FRAP activity) in seeds were indicated and phylogenetic analysis (cpDNA;trnL-F region) of twenty native grape cultivars were investigated to construct their phylogenetic tree. According to reported data on antioxidant activity and content of phytochemicals, all cultivars exhibited different values from each other, but Rutik and Gadüv cultivars were found as significantly higher in comparison to others. According to bioinformatics analysis, twenty grape cultivars were distributed into six different major groups. Rutik and Sevkeye cultivars exhibit significant distinction from other grape cultivars. The phylogenetic analysis was also associated and supported with the results of obtained data from bioactivity. The bioactivity and phylogenetic analysis were firstly identified and quantified in these grape cultivars, however, with regard to obtained data from the current study, the grape cultivars grown in Siirt province were indicated significant and valuable results and as a result, these cultivars have to be evaluated before extinction.Öğe Bitki Gelişimini Tetikleyen Rizobakterilerin Uygulandığı Buğdayda (Triticum aestivum L.) Kuraklık Stresi ileİlişkili Bazı Genlerin İfade Seviyesinin Ölçülmesi(2021) İnal, Behçet; Bektaş, Harun; Mirzapour, Mohsen; Altıntaş, Serdar; Çığ, Fatih; Cengiz, Mustafa; Sonkurt, MehmetEkmeklik buğday (Triticum aestivum L.) temel besin kaynağı olması ve tüm dünyada üretimi yapılabilen bir ürünolması nedeniyle sürdürülebilir tarım açısından en önemli bitki türlerinden biridir. Buğday bitkisinin genetik yapı olarakmısır, çeltik ve diğer tüm tarımsal ürünlerden daha kompleks bir yapıya sahip olması bu türün ıslahını zor ve uzun zamanalan bir süreç haline getirmektedir. Diğer taraftan verim değerlerinin istenilen noktalara getirilebilmesi buğdayın çevreselfaktörlere verdiği tepkilerin anlaşılması ile mümkün olabilmektedir. Bu çalışmada da buğday ıslahında en sık karşılaşılansorunlardan kuraklık ve hastalıklara karşı direncin ACC deaminaz etkisi gösteren PGPB (Plant Growth Promoting Bacteria)ile ilişkisi incelenmiştir. Çalışmamızda ACC deaminaz sentezleyen bakterilerin iki farklı ekmeklik buğday çeşidinde (Gerek79, Bezostaja 1) ve kuraklık koşullarındaki etkisi incelenmiştir. Çalışma ile ACC deaminaz etkisi ile kuraklığa karşıdayanıklılık mekanizmasında rol alan bazı transkripsiyon faktörlerin ifade seviyeleri q-RT PCR ile ölçülmüştür. Ayrıca heriki buğday genotipinde glutatyon redüktaz seviyesi ölçülerek genler ile olan ilişkisi ortaya konulmuştur. Çalışma sonucundaelde edilen veriler değişen etkinlik derecesine sahip olmakla birlikte PGPB bakterilerinin kuraklık stresinin olumsuzetkilerini azaltıcı etkiye sahip olduğu bulunmuştur.Öğe Determination of Botanical Origin and Mineral Content of Propolis Samples from Balveren (Şırnak) Beekeepers Accommodation Areas(2022) Fidan, Mehmet; Pınar, Süleyman Mesut; Erez, Mehmet Emre; İnal, Behçet; Eroğlu, HüseyinResearches on bee products have become popular in recent years. In fact, the content and component of bee products varies depending on many ecological and floristic factors and its nutritional and therapeutic properties are directly related to its content. Balveren (Şırnak province) beekeepers place their hives in locations with different geographical structure, floristic and topographic characteristics. This variability not only affects the quality of honey but also changes the properties of propolis. Studies on propolis, known as bee glue, have gained importance in recent years. As with other bee products, the propolis content also depends on the floristic characteristics of the region. In this study, propolis samples were collected from the regions where Balveren beekeepers stayed and their botanical origins, wax ratios, phenolic content, and mineral substance contents were analyzed. In the microscopic analysis, pollen grains belonging to 14 different families used by bees were determined. It was determined that the total phenolic and mineral contents of propolis vary completely depending on the location. With this study, the propolis properties of the hives in the region were tried to be revealed and it was aimed that this study would help the region's propolis to be used for technological and therapeutic purposes.Öğe DETERMINATION OF WATER-EFFICIENCY RELATIONSHIPS AND SILAGE QUALITY CHARACTERISTICS OF THE MAIZE SPECIES FOR SILAGE(ZEA MAYS L.)THE FIRST PRODUCT GROWN UNDER SEMI-ARID CLIMATE CONDITIONS(2016-10-28) Uçak, Ali Beyhan; Gençoğlan, Cafer; Bağdatlı, M.Cüneyt; Turan, Nizamettin; Arslan, Hüseyin; İnal, BehçetIn this study, a field study was carried out to determine the effect of different irrigation water amounts on dry matter efficiency and silage quality features of species of corn for silage P32K61, P31Y43, P30B74 and the relationship of water and dry matter, as well as the threshold value of the dry substance to be used in silage quality estimation by leveraging such relationship. The study was planned as three repeats in a trial pattern of divided parcels in randomized blocks. Irrigation program was established by reapplication of 100% (I100), 70% (I70), 35% (I35) of the water consumed every 7 days with the drip irrigation method. Thus, the irrigation consists of 1 full and 2 different deficit irrigation. In the study, irrigation water amount applied to I100,I70 and I35 of types P32K61, P31Y43 and P30B74 was 637-653-666; 491-495-509; 342-363-371 mm, respectively, seasonal plant water consumption values were 705-714-738; 559-554-583mm, dry matter efficiency values ranged from 24.38-24.29- 32.36, 23.26-23.33-25.5, and 12.8-14.46-14.13 t ha- 1 . Linear relations were determined between dry matter (DM) efficiency of the species and irrigation water (I) as DM=20.57I+6369(r2=0.997**), DM=30.95I+4340(r2=0.999**),Y=36.14I+5826 (r2=0.998**);and between dry matter-plant water consumption (ETa) values as Y=26.02ETa+832.1(r2=0.969**),Y=36.55ETa- 22.83 (r2=0.995**), Y=42.75ETa-1949 (r2=0.997**). The highest and lowest protein amounts by irrigation were 8.67% in the interaction of I100 irrigation and P32K61 species and 6.14% in the interaction of I35 irrigation and P31Y43 species, respectively; digestible dry matter ratio was 70% in the interaction of I100 irrigation and P30B74 species and 60% the interaction of I35 irrigation and P31Y43,respectively. No statistically significant relation between the ADF (Acid Detergent Fiber) and NDF (Neutral Detergent Fiber) values was found. The highest water consumption efficiency was 4.38 kg/da-mm in I100 irrigation and 3.37 kg/damm in I35 irrigation. In addition, thecorrelation coefficient between ET, dry matter and protein amount was r 2 :0.81** and r 2 :0.80**, and a statistically significant positive relationship was observed (p<0.01) between ETa, dry matter and protein amount. As a result of statistical and economic analyses, threshold dry matter efficiency value on which the silage quality starts to drop was determined at 25.5 t ha-1 in I70 irrigation.Öğe In silico analysis of drought responsive transposons and transcription factors in Solanum tuberosum L.(2019) Tüfekçi, Ebru Derelli; İnal, BehçetPotato (Solanum tuberosum L.) is the most important non-grainfood crop and is essential forglobal food security. Drought is one of the major abiotic stress factors resulting in huge yieldloss in the production of crops and similarly, it negativelly affects the tuberization, tuberyield and tuber quality of potato. Transposable elements (TEs) account for a large portion ofthe genome in many eukaryotic species. Several studies have identified the molecularmechanism that cause the activation of TEs under stress. Stresses and environmentalchallenges, in particular, are known to alter the expression or stimulate the transposition ofmobile elements in plants. Transcription of these stress-responsive genes is largelycontrolled by transcription factors (TFs). A number of transcription factors playing anessential role in drought tolerance of plants have been identified in the past few years. Inthis work, a subset of drought responsive TE families and TFs in potato at tuber bulking stagewas defined, based on genome-wide transposon homology and annotation. Our resultsindicated that, the read numbers for TE subfamilies yielded different distributions betweenDNA and RNA transposons. In addition, many TFs such as bHLH, WRKY, NAC, AP2/ERF mayhave important functions in regulation of drought tolerance in potato. Identification of TEsand TFs which are taking part in stress can offer useful information for functional genomicsand designing novel breeding strategies for developing stress tolerant plants.Öğe Investigation of the Presence of mecA and mecC Genes and Antibiotic Resistance Profiles in Methicillin-Resistant Staphylococcus aureus Strains Isolated from Clinical Samples(2024) Erdoğan, Mustafa; Acer, Ömer; İnal, BehçetObjective: Methicillin-resistant Staphylococcus aureus (MRSA) is widely regarded as one of the most frequent bacteria, causing a wide range of infections in humans and animals. MRSA is associated with significant morbidity and mortality in many parts of the world. The aim of this study was to determine the molecular identification, antibiotic resistance profiles, and presence of mecA and mecC genes of MRSA strains isolated from clinical specimens at Siirt Training and Research Hospital. Methods: In our study, we isolated 20 coagulase positive S. aureus strains from patients admitted to our hospital between July 2020-July 2021. Antibiotic susceptibility tests were carried out on the bacteria that were isolated and identified by culturing various clinical samples. The mecA and mecC genes were then examined by polymerase chain reaction (PCR) using the universal primers mecA-F-mecA-R and mecC-F-mecC-R following MRSA had been identified in the cultures from the clinical samples. To identify the isolated S. aureus strains by 16S ribosomal ribonucleic acid (rRNA) gene analysis, polymerase chain reaction (PCR) amplification was conducted using universal primers 68f and 518r. Results: We isolated and identified 20 coagulase positive S. aureus strains from patients admitted to our hospital. According to the 16S rRNA gene sequences, the strains isolated in this this study, exhibited high similarity (99%-100%) to the 16S rRNA genes of S. aureus strains listed in GenBank (https ://ww w.ncb i.nlm .nih. gov/g enban k/). While the mecA gene was found in 18 of 20 strains, none of the strains had the mecC gene. A high percentage of MRSA was found to be penicillin resistant (75%). In conclusion, 20 MRSA strains were isolated from various clinical specimens. Eighteen of these strains were also identified molecularly by 16S rRNA sequence analysis. Conclusion: The results of this study confirmed the significance of the 16S rRNA, mecA, and mecC genes in MRSA identification and highlighted the increasing frequency of MRSA in TürkiyeÖğe Mitigation of Drought Stress in Wheat by Bio-priming by PGPB Containing ACC Deaminase Activity(2022) Çığ, Fatih; Erman, Murat; İnal, Behçet; Bektaş, Harun; Sonkurt, Mehmet; Mirzapour, Mohsen; Ceritoğlu, MustafaOut of stress management strategies used for drought, inoculation of plant growth-promoting bacteria holds a major position due to sustainable, low-cost, and versatile properties. The plant growth-promoting bacteria, particularly containing 1-aminocyclopropane-1-carboxylic acid deaminase activity, have a critical location since they restrict ethylene synthesis under stress conditions thereby improving stress tolerance index. In this experiment, seeds of two wheat cul- tivars were primed with three bacterial strains and seedlings were grown under stress and non- stress conditions. The study was laid out in completely randomized factorial design with three replications. While plant growth achieved top performance with synthetic fertilizer in 80% of field capacity, increasing drought stress restricted the efficiency of synthetic fertilizer. In contrast, plant growth-promoting bacteria-priming promoted plant growth and dry matter accumulation under optimum and drought conditions. Increase of dry matter accumulation in treatments as con- trol plants varied between 17.1% and 57.1% under 80% of field capacity while it changed between 0.2% and 35.1% under drought conditions. TV126C and TV24C induced stress tolerance index in sensitive and tolerant cultivars under drought and optimum conditions. In conclusion, it is con- sidered that bio-priming with plant growth-promoting bacteria involving 1-aminocyclopropane- 1-carboxylic acid deaminase enzyme activity might be an effective and sustainable management strategy to drought stress in wheat cultivation.Öğe Siirt İlinde Yetiştirilen Bazı Üzüm ÇeşitlerininTanımlanması ve Kalite Değerlerinin Belirlenmesi(2017) Erez, Mehmet Emre; Fidan, Mehmet; Pınar, Süleyman Mesut; İnal, Behçet; Kaya, Yılmaz; Altıntaş, SerdarBu çalışmada,Siirt ilinde yetiştirilen üzüm çeşitlerinin belirlenmesi ve tanıtılması amaçlanmıştır. Siirt merkez, Eruh, Pervari, Şirvan, Kurtalan ve Tillo (Aydınlar) ilçelerinde yetiştirilen 20 farklı üzüm çeşidinin morfolojiközellikleri ile pH, suda çözünebilirkuru madde (SÇKM) miktarı,klorofil ve karotenoid değerleri tespit edilmiştir. Ayrıca üzüm çeşitlerine aitçekirdeklerinmorfolojik farklılıklarının tanımlanmasında bilgisayar tanımlama programından yararlanılmıştır. Elde edilen sonuçlara göre;Şirvan ve Pervari bölgesi üzümlerinin genel olarak diğer bölgelere göre yüksek pH ve kuru madde miktarlarına sahip oldukları,ancak Eruh ve Siirt Merkez bölgesindeyetişen çeşitlerde asitliğin daha yüksek olduğu tespit edilmiştir. SÇKM değerlerininise%12-24 (Kıtılnefs-Mevazer) arasında değiştiği saptanmıştır. Gadüv, Karrot ve Heseni çeşitlerinin klorofil ve karotenoid değerlerinin diğer üzüm çeşitlerine göre daha yüksek olduğu saptanmıştır. Üzüm çekirdeklerindeki morfolojik farklılıkların tanımlanması amacıyla gerçekleştirilen bilgisayar tabanlı tanımlama işleminde,en yüksek başarı oranı “Lojistik Model Tree” (LMT)(% 91.66)modelinden elde edilmiştir.Öğe The Effect of Plant Growth Promoting Rhizobacteria on Root Growth in Bread Wheat (Triticum aestivum L.)(2021) Bektaş, Harun; İnal, Behçet; Sonkurt, Mehmet; Çığ, Fatih; Bektaş, YaseminBread wheat (Triticum aestivum L.) is the most produced cool-season cereal in the worldand meets about 20% of our daily caloric intake. Climate change negatively affects grain yield, it is,therefore, necessary to improve climate-resilient wheat crops. It is a known fact that subsoil parametersare not mostly included in the breeding selection criteria due to some technical limitations. For thisreason, it is essential to examine the root system, which has a fundamental role in drought tolerance,for morphological, anatomical, physiological, and architectural aspects, to understand the geneticmechanisms of these traits and to determine breeding strategies. In this study, the seeds of twodifferent bread wheat varieties were inoculated by three different plant growth-promotingrhizobacteria (PGPR), which synthesize the ACC deaminase enzyme. When the results were evaluated,significant differences were observed between varieties and bacterial applications for the total rootlength and root growth angle. As a result of the study, it was observed that all three bacteria specieshad a positive effect on root development. Brevibacillus choshinensis was the most effectiveinoculation on total root length in Gerek 79 (95.4 cm), while it was Arthrobacter agilis in Bezostaja 1(62.8 cm). We suggest that plant growth-promoting rhizobacteria have a positive effect on wheat rootdevelopment and a detailed analysis of this effect should be carried out with future studies.Öğe The Effects of Salicylic Acid Applications on miRNA Expression in Wheat Cultivars under Drought Stress(2020) Tüfekçi, Ebru Derelli; İnal, BehçetWheat cultivation in Turkey, is highly affected by environmental factors such as drought stress, which reduces yields significantly.Applying chemicals that stimulate plant growth is an easy, low-cost, low-risk and effective approach to increase stress tolerance, andsalicylic acid is prominent in adapting plants to adverse environmental conditions such as drought stress, salinity, and improving plants'tolerance to stress. In the study, Gün 91 and Ankara 98 cultivars were used as drought tolerant and Ankara 98the sensitive plant material,respectively. Two different doses (0.1 mM, 0.5mM) of salicylic acid (SA) were applied to these plants. Drought stress teratment wasperformed one week after SA application. Total RNAs were isolated from leaf samples collected from application and control pots. Theexpression levels of miR156, miR169, miR172, miR319, mir398 and the genes targeted by these miRNAs were determined. Accordingto the results, in Gün 91, the expression levels of miR156 and miR172 was found higher in leaf tissues treated with SA under droughtstress conditions. On the other hand, the level of miR169 was higher in Ankara 98. In Gün 91, miR319 expression level was higher in0.5 mM salicylic acid + drought treatment, whereas in Ankara 98 was higher in 0.1 mM SA + drought treatment.According to the control group, mir398 expression level decreased significantly in both 91 and Ankara 98 plant groups in which SA +drought stress was applied together. As a result of this study, it was emphasized that salicylic acid is an important signal molecule inresponse to stress and it mitigates the effect in stress conditions, and the tolerance mechanism of drought tolerant and sensitive cultivarswith salicylic acid application were different.
