Browsing by Author "Baloğlu, Mehmet Cengiz"

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Cloning of Wheat (Triticum Aestıvum) Tanach 69-1 Gene and Transformation of Wheat Inflorescence by Particle Bombartment
(METU, 2009) Baloğlu, Mehmet Cengiz; Kalemtaş, Gülsüm; Eroğlu, Ayten; Battal, Abdülhamit; Öktem, Hüseyin Avni; Yücel, Meral
Comprehensive Investigation of Cucumber Heat Shock Proteins under Abiotic Stress Conditions: A Multi-Omics Survey.
(2023-07-28) Unel, Necdet Mehmet; Baloğlu, Mehmet Cengiz; Altunoglu, Yasemin Çelik
Heat-shock proteins (Hsps) are a family of proteins essential in preserving the vitality and functionality of proteins under stress conditions. Cucumber (Cucumis sativus) is a widely grown plant with high nutritional value and is used as a model organism in many studies. This study employed a genomics, transcriptomics, and metabolomics approach to investigate cucumbers' Hsps against abiotic stress conditions. Bioinformatics methods were used to identify six Hsp families in the cucumber genome and to characterize family members. Transcriptomics data from the Sequence Read Archive (SRA) database was also conducted to select CsHsp genes for further study. Real-time PCR was used to evaluate gene expression levels under different stress conditions, revealing that CssHsp-08 was a vital gene for resistance to stress conditions; including drought, salinity, cold, heat stresses, and ABA application. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of plant extracts revealed that amino acids accumulate in leaves under high temperatures and roots under drought, while sucrose accumulates in both tissues under applied most stress factors. The study provides valuable insights into the structure, organization, evolution, and expression profiles of the Hsp family and contributes to a better understanding of plant stress mechanisms. These findings have important implications for developing crops that can withstand environmental stress conditions better.
Differential Expression and Functional Analysis of Plasma MicroRNAs in the Pathogenesis of Non-segmental Vitiligo.
(2022-11-11) Pektaş, Suzan Demir; Kara, Murat; Doğan, Gürsoy; Pektaş, Mehmet Bilgehan; Baloğlu, Mehmet Cengiz; Sadi, Gökhan
Vitiligo is a disease characterized by acquired depigmentation, white macules, and patches on the skin due to the dysfunction of epidermal melanocytes. In this study, we attempt to profile the microRNA (miRNA) expression patterns and predict the potential targets, assessing the biological functions of differentially expressed miRNAs in the blood of generalized vitiligo patients. Peripheral blood samples were taken from all participants, and the expression levels of 89 identified miRNAs were analyzed with real-time quantitative polymerase chain reaction (PCR). The results indicated significant upregulation of six miRNAs and downregulation of 19 miRNAs in the plasma of vitiligo patients. The top three upregulated miRNAs were hsa-miR-451a, hsa-miR-25-3p, and hsa-miR-19a-3p, and the top three downregulated miRNAs were hsa-miR-146a-5p, hsa-miR-940, and hsa-miR-142-3p. Moreover, the miRNA expression profiles of patients with Type 3 and Type 4 phototypes were substantially different in such a way that the patients with Type 3 phototype would be more prone to the emergence of melanoma and cancer. While significant variations in the expression patterns of miRNAs in male and female vitiligo patients were demonstrated, miR-let-7i-5p, miR-19a-3p, miR-25-3p, and miR-451a were commonly upregulated, and miR-142-3p and miR-146a-5p were commonly repressed in both sexes. This study may shed light on the roles of differentially expressed miRNAs in vitiligo patients by examining the miRNA expression patterns and the combined effects of miRNA and their predicted targets.
Differential gene expression in liver tissues of streptozotocin-induced diabetic rats in response to resveratrol treatment.
(2015-04-23) Sadi, Gökhan; Baloğlu, Mehmet Cengiz; Pektaş, Mehmet Bilgehan
This study was conducted to elucidate the genome-wide gene expression profile in streptozotocin induced diabetic rat liver tissues in response to resveratrol treatment and to establish differentially expressed transcription regulation networks with microarray technology. In addition to measure the expression levels of several antioxidant and detoxification genes, real-time quantitative polymerase chain reaction (qRT-PCR) was also used to verify the microarray results. Moreover, gene and protein expressions as well as enzymatic activities of main antioxidant enzymes; superoxide dismutase (SOD-1 and SOD-2) and glutathione S-transferase (GST-Mu) were analyzed. Diabetes altered 273 genes significantly and 90 of which were categorized functionally which suggested that genes in cellular catalytic activities, oxidation-reduction reactions, co-enzyme binding and terpenoid biosynthesis were dominated by up-regulated expression in diabetes. Whereas; genes responsible from cellular carbohydrate metabolism, regulation of transcription, cell signal transduction, calcium independent cell-to-cell adhesion and lipid catabolism were down-regulated. Resveratrol increased the expression of 186 and decreased the expression of 494 genes in control groups. While cellular and extracellular components, positive regulation of biological processes, biological response to stress and biotic stimulants, and immune response genes were up-regulated, genes responsible from proteins present in nucleus and nucleolus were mainly down-regulated. The enzyme assays showed a significant decrease in diabetic SOD-1 and GST-Mu activities. The qRT-PCR and Western-blot results demonstrated that decrease in activity is regulated at gene expression level as both mRNA and protein expressions were also suppressed. Resveratrol treatment normalized the GST activities towards the control values reflecting a post-translational effect. As a conclusion, global gene expression in the liver tissues is affected by streptozotocin induced diabetes in several specific pathways. The present data suggest the presence of several processes which contribute and possibly interact to impair liver functions in type 1 diabetes, several of which are potentially amenable to therapeutic interventions with resveratrol.
Effect of drought stress on the antioxidant systems of two sunflower (Healintus annuss) cultivars
(ESCPB, 2006) Kavas, Musa; Kalemtaş, Gülsüm; Akcay, Ufuk C.; Bayrak, Abdullah T.; Özgür, Ebru; Baloğlu, Mehmet Cengiz; Ercan, Oya; Yücel, Meral; Öktem, Hüseyin Avni
EXPRESSION ANALYSIS OF NAC TYPE TRANSCRIPTION FACTORS ON WHEAT SEEDLINGS UNDER ABIOTIC STRESS CONDITIONS
(ODTÜ, 2011) Baloğlu, Mehmet Cengiz
Wheat is the most important grain crop grown in our country providing greatest part of the daily nutritional requirement. Abiotic factors including salinity, drought, cold and heat stresses affect quality and yield of wheat varieties used for the production of both bread and pasta flour. NAC proteins form one of the widest families of plant specific transcription factors. Members of this family are related with development, defense and abiotic stress responses. TaNAC69-1 and TtNAM-B2 genes were isolated from T.aestivum and T.turgidum, respectively. Then they were cloned into different monocot and dicot expression vectors to be used for further wheat and tobacco genetic transformation studies. To understand effects of salinity, drought, cold and heat stresses on expression profiles of TaNAC69-1 and TtNAM-B2 genes, quantitative real time PCR was performed. The time series expression profiles of TaNAC69-1 show that it was significantly up-regulated following by salt, drought, cold and heat stress treatments. v Except for heat stress, expression of TtNAMB-2 gene also significantly induced under drought, salt and cold stress conditions. Microarray analysis also performed to indicate effects of cold and heat stress treatments on global gene expression profiles of wheat. Differentially regulated genes show that temperature changes directly affected a large and complex transcriptional network associated with defense, metabolism and development. Genes involved in cold stress-responsive and different cold acclimation proteins were extremely up-regulated upon exposure to cold stress. Both expression levels of small and large sub-unit heat shock proteins significantly increased following heat stress period. In addition to these protective agents, transcription factors also played a central role to deal with severe effects of low and high temperature conditions. Buğday günlük besin ihtiyacının büyük bir kısmını sağlayan, ülkemizde yetiştirilen en önemli tahıl ürünüdür. Tuzluluk, kuraklık, soğuk ve sıcak streslerini içeren abiyotik faktörler, hem ekmeklik hem de makarnalık un üretiminde kullanılan buğdayın kalitesini ve verimini etkilemektedir. NAC proteinleri bitkiye özel transkripsiyon faktörlerinin en geniş ailelerinden birini oluşturmaktadır. Bu ailenin proteinleri gelişim, savunma ve abiyotik stres tepkileriyle ilişkilidir. TaNAC69-1 ve TtNAM-B2 genleri sırasıyla T.aestivum ve T.turgidum’ dan izole edilmiştir. Daha sonra, ileride yapılacak olan buğday ve tütün genetik transformasyon çalışmalarında kullanılması için, genler ayrıca farklı tek çenekli ve çift çenekli bitkilere özgü ifade vektörlerine klonlanmıştır. Tuz, kuraklık, soğuk ve sıcak streslerinin, TaNAC69-1 ve TtNAM-B2 genlerinin ifade profillerine etkilerini anlamak için, kantitatif gerçek zamanlı PZR yapılmıştır. Zamana bağlı TaNAC69-1 geninin ifade profili, TaNAC69-1 geninin ifadesinin tuz, kuraklık, soğuk ve sıcak stres uygulamalarını takiben önemli derecede arttığını göstermiştir. Sıcaklık vii stresi dışında, TtNAM-B2 geninin ifadesi de tuz, kuraklık, ve soğuk stresi dudurumları altında önemli derecede artmıştır. Soğuk ve sıcak stres uygulamalarının buğdayın genel gen ifade profili üzerine etkisini göstermek için microarray analizi de yapılmıştır. Farklı düzenlenen genler, sıcaklık değişimlerinin savunma, metabolizma ve büyümeyle ilişkili büyük ve karmaşık bir transkripsiyon ağını direk olarak etkilediğini göstermiştir. Soğuk stresine cevap veren ve farklı soğuk alıştırma proteinlerini kodlayan genlerin, soğuk stresine bağlı olarak aşırı derecede gen ifade seviyeleri artmıştır. Hem küçük hem de büyük alt üniteli ısı şok proteinlerinin gen ifade analizleri sıcaklık stresi periyodunu takiben önemli derecede atrmıştır. Bu koruyucu moleküllere ilaveten, transkripsiyon faktörleri de düşük ve yüksek sıcaklık koşullarının şiddetli etkileriyle mücadelesinde önemli bir rol oynamıştır
Farklı Sıcaklık Uygulamalarının Türk Mercimek Çeşitlerinde Antioksidan Korunma Sistemi Üzerine Etkileri
(Türk Biyokimya Dergisi, 2010) Baloğlu, Mehmet Cengiz; Ercan, Oya; Kalman, Özge; Yaşar, Osman; Öktem, Hüseyin Avni; Yücel, Meral
Mercimek, yüksek protein, folik asit ve lif içeriğiyle insan beslenmesinde oldukça önemli bir yer tutar. Türkiye dünyada mercimek üretiminde ilk sıralarda yer almakta ve ülke tüketimi için de yüzyıllardır tarımı yapılmaktadır. Kurağa ve yüksek sıcaklıklara oldukça toleranslı olmasına rağmen büyüme sezonunda orta seviyede neme ihtiyaç duyar. Türkiye’de mercimek üretimi Doğu, Güneydoğu ve İç Anadolu bölgelerinde yapılmaktadır. Bu çalışmada yazlık (Meyveci) ve kışlık (Kafkas) olmak üzere iki mercimek çeşidinin farklı sıcaklıklarda gösterdikleri büyüme geriliği, oksidatif hasar ve antioksidan tepki karşılaştırıldı. 9 günlük mercimek tohumları farklı sıcaklık uygulamalarına (25 ˚C, 35˚C ve 40˚C )2 gün maruz bırakıldı ve çeşitli fizyolojik ve biyokimyasal parametrelerde meydana gelen değişimler incelendi. Kafkas çeşidi yüksek sıcaklıklarda su kaybı gösterirken yazlık çeşit meyvecide önemli bir değişiklik gözlenmedi. 2 gün boyunca 40 ˚C uygulaması iki çeşitte de gövdede büyüme geriliğine sebep olurken, kökte anlamlı bir değişim meydana gelmedi. İyon sızıntısı ve lipid peroksidasyonu sonuçlarının gösterdiği gibi 40˚C uygulaması, meyvecide daha belirgin olmak üzere, iki çeşitte de hücre zarı hasarına sebep oldu. Yüksek sıcaklıklara maruz bırakılma nedeniyle önemli miktarda biriken prolin, Kafkas türünde daha az belirgin görülen membran hasarına sebep gösterilebilir. Askorbat peroksidaz (APX) ve Katalaz (KAT) enzimlerinin antioksidan aktivite ölçümleri iki çeşitte de benzer sabitlikte bir profil çizmiştir. Bu durum bazı ozmokoruyucu moleküllerin ve enzimatik olmayan antioksidan moleküllerin yüksek sıcaklıklarda antioksidan savunma sisteminde daha önemli rollerinin olabileceğini düşündürmektedirler.
Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration.
(2016-02-01T00:00:00Z) Kavas, Musa; Baloğlu, Mehmet Cengiz; Atabay, Elif Seda; Ziplar, Ummugulsum Tanman; Daşgan, Hayriye Yıldız; Ünver, Turgay
Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon-intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.
Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses.
(2022-01-23) Altunoğlu, Yasemin Çelik; Keleş, Merve; Can, Tevfik Hasan; Baloğlu, Mehmet Cengiz
Heat shock protein ( gene family members in the watermelon genome were identified and characterized by bioinformatics analysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed. In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to the Hsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100 family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar motif patterns. When the estimated 3-dimensional structures of the Hsp proteins were examined, it was determined that the α-helical structure was dominant in almost all families. The most orthologous relationship appeared to be between watermelon, soybean, and poplar in the gene families. For tissue-specific gene expression analysis under combined stress conditions, expression analysis of one representative gene each from root, stem, leaf, and shoot tissues was performed by real-time PCR. A significant increase was detected usually at 30 min in almost all tissues. This study provides extensive information for watermelon Hsps, and can enhance our knowledge about the relationships between genes and combined stresses.
LC-MS/HRMS Analysis, Anti-Cancer, Anti-Enzymatic and Anti-Oxidant Effects of Extracts: A Potential Raw Material for Functional Applications.
(2021-12-16T00:00:00Z) Sinan, Kouadio Ibrahime; Akpulat, Uğur; Aldahish, Afaf A; Celik Altunoglu, Yasemin; Baloğlu, Mehmet Cengiz; Zheleva-Dimitrova, Dimitrina; Gevrenova, Reneta; Lobine, Devina; Mahomoodally, Mohamad Fawzi; Etienne, Ouattara Katinan; Zengin, Gokhan; Mahmud, Shafi; Capasso, Raffaele
is a great tropical plant and is widely used for various traditional purposes. In the present study, we examined the influence of solvents (dichloromethane, ethyl acetate, methanol and infusion (water)) on chemical composition and biological capabilities of . An UHPLC-HRMS method was used to determine the chemical characterization. The biological ability was examined for antioxidant, enzyme inhibitory and anti-cancer effects. To evaluate antioxidant effects, different chemical methods (ABTS, DPPH, CUPRAC, FRAP, metal chelating and phosphomolybdenum) were applied. With regard to enzyme inhibitory properties, cholinesterases, amylase, glucosidase and tyrosinase were used. The MDA-MB-231 breast cancer cell line was chosen to determine anticancer activity. Based on the UHPLC-HRMS analysis, 37 specialized metabolites were dereplicated and identified in the studied extracts. Results revealed the presence of 15 hydroxybenzoic, hydroxycinnamic, acylquinic acids, and their glycosides, one rotenoid, seven flavonoids, 12 fatty acids and two other glycosides. Among the tested extracts, the methanol extract showed a stronger antioxidant ability compared with other extracts. The methanol extract also showed the best inhibitory effects on tyrosinase and glucosidase. In the anti-cancer evaluation, the methanol extract showed stronger anticancer effects compared with water extract. In summary, our observations can contribute to the establishment of as a potential candidate for functional applications in the preparation.
Molecular Cloning and Characterization of Ubiquitin Conjugating Enzyme (E2) from melon (Cucumis melo L.) and Evolutionary Relationships among E2s in Plants
(HIBIT 2010 The Fifth International Symposium on Health Informatics and Bioinformatics, 2010) Baloğlu, Mehmet Cengiz; Zakharov, Florence Negre; Öktem, Hüseyin Avni; Yücel, Meral
NAC69-1 ve NAM-B2 Genlerinin Buğdaydan İzolasyonu ve Karakterizasyonu
(XVI. ULUSAL BİYOTEKNOLOJİ KONGRESİ 2009, 2009) Öktem, Hüseyin Avni; Çökmüş, Cumhur; Eyioğan, Fisun; Tuncer, Serdar; Baloğlu, Mehmet Cengiz; Ercan, Oya; Özer Uyar, Ebru
Bu çalışmada, NAC tipi transkripsiyon faktörlerinden NAC69-1 ve NAM-B2 genlerinin buğdaydan izolasyonu yapılmıştır. Ayrıca bu genlerin buğdayda yüksek düzeyde ifade edilebilmesini sağlamak amacıyla, genler uygun vektörlere klonlanmıştır. NAC69-1 geni yazlık bir buğday çeşidi Triticum aestivum L. cv. (Yüreğir-89)’dan, NAM-B2 geni ise kışlık bir buğday çeşidi, Triticum turgidum spp. durum cv. (Kızıltan-91)’dan izole edilmiştir. Total RNA izolasyonu trizol reaktifi kullanılarak gerçekleştirilmiştir. Elde edilen RNA’nın kalite ve miktarı spektrofotometre yardımıyla ölçülmüştür. cDNA sentezi için Fermentas’ın RevertAid First Strand cDNA Synthesis Kit’i kullanılmıştır. PZR sonucunda çıkan ürünler %1’lik agaroz jelde yürütülmüş ve beklenen büyüklükte görülen bantlar kesilerek jelden ayrıştırılmıştır. Ayrıştırılan bu genler, CloneJETTM PCR Cloning Kit’te verilen protokole uygun olarak pJET1.2 klonlama vektörüne transfer edilmiştir. Bu vektörde bulunan genler çift yönde sekanslamaya gönderilmiştir. Klonlanan TaNAC69-1 ve TtNAM-B2 genleri NCBI’da bulunan sekanslarla %100 benzerlik göstermiştir. Genler monokot bitkiler için kullanılan ekpresyon vektörlerinden Impact Vector 1.1. (Plant Research International, Wageningen University, UR) ve pAHC25’e aktarılımıştır. Impact Vector 1.1’de Rubisco (Ribulose bisphosphate carboxylase) promoter ve terminatör bulunurken, pAHC25’te ise bar ve uidA (GUS) markör genlerini içermektedir ve her ikisi de ayrı ayrı Ubi1 promotoru ile kontrol edilmektedir. TaNAC69-1 ve TtNAM-B2 genlerini içeren Impact Vector 1.1 ve pAHC25 vektörleri “Obitek-Biolab Biobalistic Gene Transfer System” partikül bombardımanı aracılığıyla buğdaydan izole edilen olgunlaşmamış başak taslaklarına aktarılmıştır
OPTIMIZATION OF REGENERATION AND AGROBACTERIUM MEDIATED TRANSFORMATION OF SUGAR BEET (Beta vulgaris L.)
(2005) Baloğlu, Mehmet Cengiz
In this study, optimization of a transformation and regeneration system via indirect and direct organogenesis in cotyledon, hypocotyl, petiole, leaf and shoot base tissues of sugar beet (Beta vulgaris L. cv. ELK 345 and 1195) was investigated. Two different germination, three different callus induction and shoot induction medium was used for indirect organogenesis of sugar beet cultivar ELK 345. Except cotyledon, other explants (hypocotyl, petiole and leaf) produced callus. However no shoot development was observed from callus of these explants. Shoot base tissue of sugar beet cultivar 1195 was employed for direct organogenesis. Shoot development was achieved via direct organogenesis using 0.1 mg/L IBA and 0.25 mg/L BA. Root development and high acclimatization rate were accomplished from shoot base tissue.
Optimization of yeast (Saccharomyces cerevisiae) RNA isolation method for real-time quantitative PCR andmicroarray analysis
(African Journal of Biotechnology Vol. 11(5), pp. 1046-1053, 16 January, 2012, 2012) Yılmaz, Remziye; Akça, Oya; Baloğlu, Mehmet Cengiz; Öz, Mehmet Tufan; Öktem, Hüseyin Avni; Yücel, Meral
Quality of the starting RNA is indispensably important for obtaining highly reproducible quantitative polymerase chain reaction (qPCR) and microarray results for all organisms as well as S. cerevisiae. Isolating RNA from yeast cells with a maximum quality was especially critical since these cells were rich in polysaccharides and proteins. The method has been optimized through modification pretreatment applications for the isolation of S. cerevisiae RNA for qPCR and microarray analysis. Two extraction assay a TRIzol reagent-based method with three pretreatment applications and a commercially available kit with own pretreatment application, were compared for this purpose. Furthermore, the concentration yeast cells and enzyme were controlled in the range of 2 × 106 to 6 × 107 cells and 0.5 to 5 mg/ml, respectively to prevent RNA yields decrease and RNA degradation. Results of RNA isolation of the middle scales of yeast cells and enzyme concentrations which obtained fluxional deduct were not discussed here. Concentration and integrity of RNA samples were determined by μL spectrophotometer and Bioanalyzer, respectively. Quality of cDNA prepared from RNA samples was inspected with amplification using 18SrRNA primers in qPCR reactions. Furthermore, quality of RNA samples were evaluated using quality control parameters associated with performance of the assay and hybridization in microarray experiments. The highest yield and quality of RNA, which was appropriate for reverse transcription, cDNA library construction, qPCR reactions and microarray hybridizations without further processing was obtained by using Protocol C which used highest yeast cell and enzyme concentrations during the pretreatment application.
Optimization of yeast (Saccharomyces cerevisiae) RNA isolation method for real-time quantitative PCR andmicroarray analysis
(African Journal of Biotechnology Vol. 11(5), pp. 1046-1053, 16 January, 2012, 2012) Yılmaz, Remziye; Akça, Oya; Baloğlu, Mehmet Cengiz; Öz, Mehmet Tufan; Öktem, Hüseyin Avni; Yücel, Meral
Quality of the starting RNA is indispensably important for obtaining highly reproducible quantitative polymerase chain reaction (qPCR) and microarray results for all organisms as well as S. cerevisiae. Isolating RNA from yeast cells with a maximum quality was especially critical since these cells were rich in polysaccharides and proteins. The method has been optimized through modification pretreatment applications for the isolation of S. cerevisiae RNA for qPCR and microarray analysis. Two extraction assay a TRIzol reagent-based method with three pretreatment applications and a commercially available kit with own pretreatment application, were compared for this purpose. Furthermore, the concentration yeast cells and enzyme were controlled in the range of 2 × 106 to 6 × 107 cells and 0.5 to 5 mg/ml, respectively to prevent RNA yields decrease and RNA degradation. Results of RNA isolation of the middle scales of yeast cells and enzyme concentrations which obtained fluxional deduct were not discussed here. Concentration and integrity of RNA samples were determined by µL spectrophotometer and Bioanalyzer, respectively. Quality of cDNA prepared from RNA samples was inspected with amplification using 18SrRNA primers in qPCR reactions. Furthermore, quality of RNA samples were evaluated using quality control parameters associated with performance of the assay and hybridization in microarray experiments. The highest yield and quality of RNA, which was appropriate for reverse transcription, cDNA library construction, qPCR reactions and microarray hybridizations without further processing was obtained by using Protocol C which used highest yeast cell and enzyme concentrations during the pretreatment application.
Particle bombardment transformation of some Turkish wheat cultivars with TaNAC69-1 and TtNAMB2 genes
(2012) Battal, A.; Baloğlu, Mehmet Cengiz; Kavas, M.; Yücel, M.; Öktem, Hüseyin Avni
Wheat is one of the most important crop plants in the world. The production of wheat is seriously affected by biotic (pests, bacterial and fungal diseases) and abiotic (drought, salinity and freezing) stresses. NAC family proteins (NAM/ATAF1-2/CUC2) are plant specific transcription factors and related with development, defense and abiotic stress responses.
Plant Gene Discovery Tecnologies
(2011) Baloğlu, Mehmet Cengiz; Negre Zakharov, F.; Öktem, H.A.; Yücel, M.
Plastidial Expression of 3β-Hydroxysteroid Dehydrogenase and Progesterone 5β-Reductase Genes Confer Enhanced Salt Tolerance in Tobacco.
(2021-10-29T00:00:00Z) Sameeullah, Muhammad; Yildirim, Muhammet; Aslam, Noreen; Baloğlu, Mehmet Cengiz; Yucesan, Buhara; Lössl, Andreas G; Saba, Kiran; Waheed, Mohammad Tahir; Gurel, Ekrem
The short-chain dehydrogenase/reductase (SDR) gene family is widely distributed in all kingdoms of life. The genes, 3β-hydroxysteroid dehydrogenase () and progesterone 5-β-reductases (, ) play a crucial role in cardenolide biosynthesis pathway in the species. However, their role in plant stress, especially in salinity stress management, remains unexplored. In the present study, transplastomic tobacco plants were developed by inserting the , and genes. The integration of transgenes in plastomes, copy number and transgene expression at transcript and protein level in transplastomic plants were confirmed by PCR, end-to-end PCR, qRT-PCR and Western blot analysis, respectively. Subcellular localization analysis showed that 3β-HSD and P5βR1 are cytoplasmic, and P5βR2 is tonoplast-localized. Transplastomic lines showed enhanced growth in terms of biomass and chlorophyll content compared to wild type (WT) under 300 mM salt stress. Under salt stress, transplastomic lines remained greener without negative impact on shoot or root growth compared to the WT. The salt-tolerant transplastomic lines exhibited enhanced levels of a series of metabolites (sucrose, glutamate, glutamine and proline) under control and NaCl stress. Furthermore, a lower Na/K ratio in transplastomic lines was also observed. The salt tolerance, mediated by plastidial expression of the , and genes, could be due to the involvement in the upregulation of nitrogen assimilation, osmolytes as well as lower Na/K ratio. Taken together, the plastid-based expression of the genes leading to enhanced salt tolerance, which opens a window for developing saline-tolerant plants via plastid genetic engineering.
Sıcaklık Stresinin Kavunda Isı Şoku Protein Genlerinin (Hsp1-Hsp2) İfadesi Üzerine Etkileri ve Proteome Analizleri
(Türk Biyokimya Dergisi, 2009) Baloğlu, Mehmet Cengiz; Karaca, Samir; Öktem, Hüseyin Avni; Yücel, Meral
Oksidatif stres mide kanseri oluşumunda önemli rol oynamaktadır. Ancak gastrik kanserlerde oksidatif strese bağlı moleküler değişimler henüz açığa çıkmamıştır. Matriks metalloproteinazlar (MMP) ekstrasellüler matriksi parçalayarak kanser hücrelerine invaziv özellik kazandırıp onları daha da agresif hale getirmekle bilinirler ayrıca kendi içlerinde regüle edildikleri de bilinmektedir. Biz de bu çalışmada H2 O2 nin mide kanserli hücre hatlarının invazyonuna etkisini araştırıp, RNA müdehalesi (siRNA) tekniği ile ilk defa gastrik kanserlerde MMP-3 genini susturarak diğer MMPleri ekspresyon düzeyinde ne yönde etkilendiğini gösterdik. Öncelikle daha agresif olduğu bilinen AGS hücrelerinin, H2 O2 muamelesi sonucu MKN-45 ve 23132/87 hücrelerine göre daha invaziv olduğu gösterildi. Buna paralel olarak MMP gen ifadesi açısından incelediğimizde çalışılan 17 MMP geninden 12 tanesinin AGS’de ifade edildiği tespit edildi. Öte yandan az faklılaşmış ve difüz tip gastrik kanser orijinli hücreler olan MKN-45’de 10 MMP’geni, 23132/87’de ise sadece 5 tane MMP geninin ifade olduğu görülmektedir. MMP’ler içerisinde sadece AGS hücresinde ifade olan ve daha çok agresifliğe yol açtığı düşünülen MMP-3 genine özgü bir RNA susturumu gerçekleştirilmiştir. MMP genlerinin ifadesinde azalış ve artışlar görülmüştür. MMP3’ün susturulması MMP-15’in ifadesini azaltırken, MMP10 ifadesini arttırmıştır. Dolayısı ile pek çok kanser türünde olduğu gibi ileri gastrik kanserde de MMP-3, diğer MMP genlerinin ifadesini etkilemesi bakımından önemli bir makır gen olmaktadır.