Proteomic basis of drought tolerance in chickpea

Thesis (Master)--Izmir Institute of Technology, Molecular Biology and Genetics, Izmir, 2010Includes bibliographical references (leaves: 56-64)Text in English; Abstract: Turkish and Englishix, 80 leavesIn this study our aim was to identify differentially expressed proteins in root and leaf samples of the drought tolerant chickpea cultivar Gokce using proteomics approaches. For this aim we carried out 2D gel electrophoresis from total proteome extracts of root and leaf samples of Gokce cultivar from drought treated and control samples. In root 2D gels we obtained approximately 430 proteins; 14 of them were newly formed and 4 of them were disappeared in drought stress. Also we obtained 12 over-expressed protein and 4 down-regulated spot as a result of drought stress. In leaf 2D gels we obtained approximately 450 proteins 4 of them were newly formed spots, and 3 of them were disappeared in drought stress. For these samples we obtained 24 over-expressed proteins and 17 down-regulated proteins in drought stress. We identified differentially expressed proteins in MALDI-TOF/TOF mass spectrometer via peptide mass fingerprinting. Identified proteins are zinc finger (C2H2 type, AN1-like) family protein, pathogenesis-related family protein, STRS2 (STRESS RESPONSE SUPPRESSOR 2), 26S proteasome non-ATPase regulatory subunit 3, pentatricopeptide repeat-containing protein, RABB1C (ARABIDOPSIS RAB GTPASE HOMOLOG B1C); serine hydroxymethyltransferase, fiddlehead protein, aluminum-activated malate transporter, phloem protein 2-A8, ribosomal protein L30 family protein, N-rich protein with known function and we identified 14 hypothetical proteins with unknown function. Identified proteins are WRKY DNA-binding protein 6, myb family transcription factor, porin family protein, pentatricopeptide repeat (PPR) protein and transmembrane protein and 2 hypothetical proteins with unknown function

Sitokinin sentez genini aşırı ifadeleyen domates bitkilerinin geliştirilmesi ve proteomik yaklaşımla karakterizasyonu

Thesis (Doctoral)--Izmir Institute of Technology, Molecular Biology and Genetics, Izmir, 2020Includes bibliographical references (leaves: 141-214)Text in English; Abstract: Turkish and EnglishCytokinins (CKs) are plant hormones controlling growth and development including cell division and differentiation, apical dominance and delay of senescence. CKs take part in regulation of the abiotic stress response in plants. In this study, transgenic tomato plants overexpressing the IPT (CK biosynthetic gene) were developed. Homozygous transgenic plants exhibited a phenotype with reduced plant stature and lost apical dominance. Increased shoot biomass and leaf water content with a reduction in fruit yield were observed in all transgenic lines. Proteomics analysis was conducted to understand high CK response in molecular level. Proteins supporting a strong sink phenotype and vasculature development were upregulated in transgenic lines and reflected the phenotypic changes observed in homozygous plants. Proteins related to stress response such as detoxification enzymes and PR proteins were upregulated in a gradual manner in transgenic lines with the strongest up-regulation in T6 homozygous line indicating the metabolic stress induced by high CK levels. The transgenic plants were tested for drought stress and observed to have improved water use efficiency, antioxidant response and delayed senescence compared to nontransgenic plants. Proteomic analyses from leaf total and nuclear enriched extracts were conducted to understand the molecular basis of improved drought tolerance. Proteins related to photosynthesis and oxidative stress response were the most prominent groups of differentially abundant proteins in the transgenic line under drought, which could contribute to tolerance. Eighteen transcription factors were differentially abundant in the nuclear proteome of drought stressed plants. These transcription factors could control the gene expression contributing to tolerance.Sitokinler (CK) hücre bölünmesi ve farklılaşması, apikaldominansi ve yaşlanmanın geciktirilmesi gibi bitki büyüme ve gelişimini kontrol eden bitki hormonlarıdır. Ayrıca bitkilerde abiyotik cevabın düzenlenmesinde de rol oynarlar. Bu çalışmada, IPT genini (CK biyosentez geni) aşırı ifade eden transgenik domates bitkileri geliştirilmiştir. Homizgot bitkilerde kısa bitki boyu ve apikal dominansın kaybı fenotipleri gözlemlenmiştir. Bütün transgenik bitkilerde yeşil aksam ağırlığında ve yaprak su miktarında artış görülürken meyve veriminin düştüğü gözlemlenmiştir. Yüksek CK tepkisinin moleküler düzeyde anlaşılması için proteomik analizler gerçekleştirilmiştir. Homozigot bitkilerdeki fenotipik değişimlere işarat edebilecek kuvvetli depo fenotipi ve iletim dokusu ile ilgili proteinlerin transgenik bitkilerde yüksek miktarda ifadelendiği tespit edilmiştir. Detoksifikasyon enzimleri ve PR proteinleri gibi stres cevabı ile iligili proteinlerin transgenik hatlarda kademeli olarak arttığı görülmüş, en fazlaartış ise T6 homozigot hattında gözlenmiştir, ki bu artış yüksek CK düzeyleri sebebi ile uyarılmış metabolik strese işaret etmektedir. Geliştirilen transgenik hatlar, kuraklık stresi için test edilmişler ve su kullanım verimi, antioksidan cevap ve geciktirilmiş yaşlanma karakteri bakımından transgenik olmayan bitkilere gore daha üsütün oldukları gözlenmiştir. Gelişmiş kuraklık toleransının moleküler düzeyde anlaşılması için yaprak total protein ve çekirdek zenginleştirilmiş özütlerinde proteomik analizler gerçekleştirilmiştir. Fotosentez ve oksidatif stres cevabı ile ilgili proteinler farklı ifadelenen proteinler arasında en öne çıkan gruplardır ve bunların kuraklık toleransı sağlanmasında etkisi olabilir. On sekiz transkripsiyon faktörünün kuraklık stresi koşulları altında farklı miktarlarda ifadelendiği tespit edilmiştir. Bu transkripsiyon faktörleri toleransa katkı sağlayan genlerin ifadelenmesini kontrol edebilirler

Proteomic basis of drought tolerance in chickpea

Thesis (Master)--Izmir Institute of Technology, Molecular Biology and Genetics, Izmir, 2010Includes bibliographical references (leaves: 56-64)Text in English; Abstract: Turkish and Englishix, 80 leavesIn this study our aim was to identify differentially expressed proteins in root and leaf samples of the drought tolerant chickpea cultivar Gokce using proteomics approaches. For this aim we carried out 2D gel electrophoresis from total proteome extracts of root and leaf samples of Gokce cultivar from drought treated and control samples. In root 2D gels we obtained approximately 430 proteins; 14 of them were newly formed and 4 of them were disappeared in drought stress. Also we obtained 12 over-expressed protein and 4 down-regulated spot as a result of drought stress. In leaf 2D gels we obtained approximately 450 proteins 4 of them were newly formed spots, and 3 of them were disappeared in drought stress. For these samples we obtained 24 over-expressed proteins and 17 down-regulated proteins in drought stress. We identified differentially expressed proteins in MALDI-TOF/TOF mass spectrometer via peptide mass fingerprinting. Identified proteins are zinc finger (C2H2 type, AN1-like) family protein, pathogenesis-related family protein, STRS2 (STRESS RESPONSE SUPPRESSOR 2), 26S proteasome non-ATPase regulatory subunit 3, pentatricopeptide repeat-containing protein, RABB1C (ARABIDOPSIS RAB GTPASE HOMOLOG B1C); serine hydroxymethyltransferase, fiddlehead protein, aluminum-activated malate transporter, phloem protein 2-A8, ribosomal protein L30 family protein, N-rich protein with known function and we identified 14 hypothetical proteins with unknown function. Identified proteins are WRKY DNA-binding protein 6, myb family transcription factor, porin family protein, pentatricopeptide repeat (PPR) protein and transmembrane protein and 2 hypothetical proteins with unknown function

Mining frequent patterns from microarray data

6th International Symposium on Health Informatics and Bioinformatics, HIBIT 2011; Izmir; Turkey; 2 May 2011 through 5 May 2011The rapid development of computers and increasing amount of collected data made data mining a popular analysis tool. Data mining research is interrelated to many fields and one of the most important ones is bioinformatics. Among many techniques, mining association rules or frequent patterns is one of the most studied techniques in computer science and it is applicable to bioinformatics. Association analysis of gene expressions may be used as decision support mechanism for finding genes that are in same pathway. In this work, publicly available yeast microarray data has been analyzed using an efficient frequent pattern mining algorithm Matrix Apriori and frequently co-over-expressed genes have been identified. © 2011 IEEE

Pros and cons of plant nuclear protein enrichment

23rd International PhD Students Conference (MendelNet); NOV 09-10, 2016; Mendel Univ Brno, Fac AgriSciencesNuclear proteome contains important regulatory proteins. To improve the detection of these proteins, Percoll gradient-based fractionation techniques have been developed and optimized. However, owing to the ever increasing sensitivity of identification methods based on liquid chromatography and mass spectrometry, the time and material consuming fractionation methods may no longer be necessary. Here, we show that a Percoll-based nuclear protein fractionation of tomato leaf proteome increased the number of detected proteins, but at least some nuclear proteins were lost or depleted in the process

Cry1Ac-mediated resistance to tomato leaf miner (Tuta absoluta) in tomato

Tomato leaf miner (Tuta absoluta) is a major pest of tomato in regions with hot climates such as South America and the Mediterranean. This insect feeds on almost every part of the plant and forms galleries while feeding on the plant’s inner tissues. Thus, it can cause plant death and is costly and difficult to control with chemical sprays. In this study, we transferred a modified Bacillus thuringiensis cry1Ac gene to tomato plants via Agrobacterium tumefaciens mediated transformation. Introduction of the cry1Ac gene to the tomato genome was confirmed with PCR and Southern blot analysis in 12 independent events. Insertion sites of the transgene in the tomato genome were determined with TAIL-PCR (thermal asymmetric interlaced polymerase chain reaction) for four selected transgenic lines. Cry1Ac gene expression was verified at both the transcriptional and translational levels, with RT-qPCR and Western blot analyses, respectively. Expression of the Cry1Ac protein in tomato resulted in T. absoluta mortality rates of 38–100% depending on transgenic line. In addition, gallery formation was reduced in 57–100% of the transgenic plants. Moreover, it was found that a single copy of the gene in the hemizygous condition is sufficient to confer tolerance to leaf miner. This is the first reported development of tomato plants resistant to T. absoluta. These transgenic plants are promising for development of commercial tomato cultivars resistant to leaf miner, which will limit the use of environmentally harmful chemicals for control of this pest.Izmir Institute of Technology (2014-IYTE-32

Water-soluble antioxidant potential of melon lines grown in Turkey

The antioxidant potential of 42 melon (Cucumis melo) lines including six cultivars grown in Turkey was assessed by measuring total water-soluble antioxidant capacity, phenolic and vitamin C contents. The lines showed significant variability for all three antioxidant parameters with breeding lines having higher antioxidant capacity and phenolic content than some popular cultivars. Different types of melons also showed significantly different antioxidant potentials. Thus, galia and ananas types showed a higher mean antioxidant capacity and phenolic content than the other tested types (yuva, kislik, canary, and charentais). Correlation analysis between antioxidant parameters showed a significant correlation between water-soluble antioxidant capacity and phenolic content. © 2012 Copyright Taylor and Francis Group, LLC.Izmir Institute of Technology (2006-IYTE-03

Development of EST-SSR markers for diversity and breeding studies in opium poppy

All publicly available opium poppy expressed sequence tag (EST) sequences, totalling 20 885, were assembled into unigenes and examined for simple sequence repeats (SSRs). Nearly 19% of the 14 957 unigenes contained SSRs with 4% harbouring more than one SSR. Average density of the SSRs was 1 SSR per 3.6 kb of non-redundant EST sequence. Trinucleotide SSRs were most frequently identified (39%), and many of the most prevalent motifs were AT-rich. Flanking primers were designed for 86% of the SSRs and 67 primer pairs were tested on 37 opium poppy accessions and seven related species. All markers were transferable to the related species. Polymorphism information content (PIC) values for the markers were intermediate for comparisons within opium poppy (average of 0.27) and slightly higher for comparisons across species (average of 0.29). The markers were found to be useful for diversity analysis as they successfully distinguished among Turkish opium poppy accessions and land races.Scientific and Technological Research Council of Turkey (109O797