Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
Browse
21 results
Search Results
Master Thesis Proteomic analysis of benzylisoquninoline alkaloid (BIA) biosynthesis in different opium poppy cultivars and examination of differentially expressed proteins in relation to bia content(01. Izmir Institute of Technology, 2024) Taşdemir, İrem; Frary, AnneHaşhaş (Papaver somniferum), eczacılıkta kullanılan benzilizokinolin alkaloidleri (BIA) üretmesi nedeniyle Türkiye için stratejik öneme sahip bir bitkidir. Yalnızca haşhaş bitkisinden elde edilebilen bu alkaloidler, ağrı kesici, öksürük kesici ve narkotik amaçlı ilaç olarak yaygın şekilde kullanılmaktadır. Türkiye'nin haşhaş çeşitleri, yüksek BIA içeriği hedeflenerek geliştirilmiş olup küresel rekabet için verimlerinin artırılması gerekmektedir. Bu çalışmada, farklı haşhaş çeşitlerinin belirli organlarındaki protein seviyelerinin değişen BIA içeriği ile ilişkili olarak karşılaştırılmasını içeren proteomik bir yaklaşım kullanılmıştır. Çalışmada, belirli alkaloidler açısından öne çıkan üç Türk haşhaş çeşidi kullanılmıştır: tebain (TMO T), morfin (Ofis 2) ve noskapin (Ofis NM). Haşhaş bitkisinin belirli dokularından alınan protein ekstraktları, LC-MS/MS kullanılarak incelenmiş ve ardından kuru kapsüllerdeki BIA miktarı TLC/HPLC analizleriyle ölçülmüştür. Bu şekilde, farklı haşhaş çeşitlerinin ve organlarının protein ekspresyon modelleri ile kapsüllerdeki alkaloid birikimi arasındaki bağlantılar araştırılmış ve BIA metabolizmasının biyosentetik ve düzenleyici yollarına dair bilgi edinilmiştir. İncelenen beş doku arasında, olgun kapsüller en yüksek sayıda anlamlı farklı şekilde ifade edilen proteini gösterirken, Ofis 2 protein ifade profilleri açısından tüm dokularda TMO T ve Ofis NM'den belirgin şekilde ayrışmıştır. BIA yolağındaki kilit enzimler, üç haşhaş çeşidinin kapsülleri ve lateks içeren gövdeleri arasında anlamlı yukarı ve aşağı regülasyon göstermiştir. Gelecekteki araştırmalar, BIA biyosentezini aydınlatmak ve manipüle etmek için karakterize edilmemiş proteinlerin işlevlerini, çoklu omik entegrasyonunu, dokuya özgü enzim lokalizasyonunu ve işlevsel gen çalışmalarını araştırabilir. Bu sayede farmasötik amaçlar için yüksek verimli haşhaş çeşitlerinin geliştirilmesine olanak sağlanabilir.Master Thesis Bacterial Cellulose Production With Gluconoacetobacter Xylinus From Hazelnut Waste(01. Izmir Institute of Technology, 2024) Gazioğlu, Metehan; Frary, Anne; Büyükkileci, Ali OğuzBakteriyel selüloz (BC), biyomedikal, kozmetik ve elektronik gibi birçok endüstriyel alanda önemli potansiyele sahip doğal bir biyopolimerdir. BC'nin özellikleri arasında yüksek yüzey alanı, sıvı ve gaz geçirgenliği, biyobozunabilirlik ve modifiye edilebilirlik bulunur. Bu çalışmada bakteriyel selüloz üretimi gluconacetobacter xylinus tarafından gerçekleştirilmiştir. BC üretimini optimize etmek için çeşitli çevresel koşullar ve besiyerleri test edilmiştir. Bu çalışmada, fındık kabuklarının asit ve baz kimyasal ön işlemleri ile elde edilen şekerlerin kullanımına odaklanılmıştır. Fındık kabuğunun kimyasal içeriği belirlenmiş ve lignin, selüloz ve hemiselüloz oranları sırasıyla %42,09, %21,84 ve %22,99 olarak bulunmuştur. Bu içerikler, farklı ön işlem yöntemlerinin etkinliğini değer- lendirmek için kullanılmıştır. Fındık kabukları, farklı kimyasallar ile ön işlem- den geçirilmiş ve şeker salınımı açısından değerlendirilmiştir. Alkali ön işlemler, şeker salınımı açısından daha etkili bulunmuştur. Özellikle, %1'lik potasyum hidroksit ve %3'lük sodyum hidroksit ile ön işlem gören numuneler sırasıyla 37,8 ve 39 g/L en yüksek şeker konsantrasyonuna sahip olmuştur. Optimiza-syon çalışmaları kapsamında inokülasyon oranı, pH değeri, gün ve etanol varlığı gibi parametreler incelenmiştir. %10 inokülasyon oranı, 10 gün ve pH 6 ile en yüksek BC verimi elde edilmiştir. Kıyaslanan kültürlere bakıldığında %1 potasyum hidroksit ile ön işlem görmüş sonrasında da besiyeri içerisinde %1'lik etanol bulunan besiyerinde 2369 mg/L' de en çok bakteriyel selüloz üretildiği belirlenmiştir. Farklı kültürlerden alınan bakteriyel selülozlarda etanol ilavesinin su tutma kapasitesini azalttığ görülmüştür. FT-IR sonuçları bütün örneklerin saf olarak elde edildiğini ve yapısal bütünlüğün korunduğu göstermiştir. Bu tez, BC üretimini optimize etmek için gerekli olan koşulları belirlemekte ve fındık kabuklarının sürdürülebilir bir şeker kaynağı olarak kullanılabileceğini göstermektedir.Master Thesis Evaluation of the Pharmaceutical Potential of Components of Aniseed and Flaxseed Against Shigellosis (shigella Sonnei) Through in Silico and in Vitro Analysis(2023) Fajembola, Tosin Felicia; Frary, AnneShigella sonnei, şigelloz (dizanteri) hastalığına neden olan bir insan patojenidir. Şu anda piyasada bulunan antibiyotiklere karşı direnci nedeniyle şigelloz, Dünya Sağlık Örgütü tarafından küresel bir kriz olarak tanımlanmıştır. Bu nedenle bu hastalığa yönelik yeni ilaç adaylarının keşfedilmesine ihtiyaç vardır. Bitki bazlı ilaç adayları, geniş çeşitlilikteki biyoaktif bileşenleri ve bitkilere genellikle kolayca erişilebilmesi ve yetiştirilmesinin ucuz olması nedeniyle dikkat çekmektedir. Anason ve keten tohumu esansiyel yağlarının çeşitli insan hastalıkları üzerinde tedavi edici etkileri olduğu gösterilmiştir. Bu araştırmada bu esansiyel yağların farmasötik potansiyeli in silico ve in vitro analizlerle değerlendirildi. Moleküler yerleştirme, moleküler dinamik simülasyonu ve ADMET analizinin sonuçları, anasondan elde edilen izoöjenol ve p-anisaldehitin ve keten tohumundan elde edilen sekoizolarisiresinolün, şikimat yolu ve T3SS ATPaz enzimlerine iyi bağlanma afiniteleri sergiledikleri ve umut verici ADMET gösterdikleri için en umut verici adaylar olduğunu gösterdi. profiller. Kalitatif inhibitör tahlili, izoöjenolün en fazla inhibitör aktiviteyi sergilediğini ve bunu p-anisaldehitin izlediğini gösterdi. Bakteri aynı zamanda SDG'ye de duyarlıydı. Kantitatif inhibisyon tahlili aynı zamanda izoöjenolün minimum inhibitör konsantrasyonu (MIC) 0,04 mg/ml ve minimum bakterisit konsantrasyonu (MBC) 0,08 mg/ml ile en güçlü bileşik olduğunu ve ardından p-anisaldehit ve SDG'yi gösterdi. Sonuç olarak, in silico ve in vitro analizler, anason ve keten tohumu esansiyel yağlarının spesifik bileşenlerinin, S. sonnei'ye karşı ilaç olarak potansiyel biyoaktiviteye sahip olduğunu gösterdi.Master Thesis Genetic Modifications of Chlorogenic Acid Content in Eggplant (solanum Melongena L.) by Agrobacterium-Mediated Transformation Technique(01. Izmir Institute of Technology, 2023) Tanyolu, Tanya Nil; Frary, AnneEggplant is a nutritious vegetable that is low in lipids and high in fiber, vitamins, and minerals. Eggplant is a good source of phenolic compounds, particularly chlorogenic acid (CGA), which is associated with several health benefits, such as reducing the risk of diabetes and cardiovascular diseases. Among CGA-rich fruits, eggplant has a geographically wide distribution while coffee is limited to tropical regions. For that reason, eggplant can be used as alternative to coffee for CGA production. The goal of this research was to develop transgenic eggplant that has increased CGA content using the Agrobacterium-mediated transformation technique. The over-expression of the Myb1 gene, which is related to CGA synthesis and responsible for the production of a transcription factor that activates the phenylpropanoid pathway in eggplant, was used. The Myb1 gene was isolated, amplified, and inserted into the PRI910 vector system before being transformed into Agrobacterium tumefaciens. After plant transformation, seven regenerated plants were verified as transgenic by PCR analysis. Young leaves from transgenic eggplants were used for mRNA expression analysis and metabolite analyses. A two-fold increase in Myb1 gene expression levels for three of the transformed plants was observed and five plants showed a significant increase in 3-CGA content. Expression of Myb1 correlated with CGA content measured by HPLC analysis. Specifically, the two-fold increases in Myb1 expression of three plants corresponded with two-fold increases in their leaf 3-CGA content. In the future, these genetically modified plants could serve a crucial role in better understanding the pathway of CGA production in eggplants, and may also prove useful in generating valuable CGAs for both economic and medicinal purposes. Subsequent research can be directed towards determining the CGA content via measurement of 5-CGA and examining CGA content in different parts of the fruit such as flesh and peel. Study of the next generation (T1 plants) will also be critical for confirming the stability of the transformation.Master Thesis Genetic Modification of Glycoalkaloid Content in Eggplant by Agrobacterium-Mediated Transformation Technique(Izmir Institute of Technology, 2022) Gültekin, Helin; Frary, AnneEggplant is one of the first plantsthat was cultivated in the Old World. It is economically and agriculturally important for many countries such as Turkey. In addition, eggplant has been used medicinally since ancient times. The medicinal effects of eggplant come from its secondary metabolites. One of the most useful secondary metabolites is steroidal glycoalkaloids (SGA). SGAs have been used in cancer treatment research. The biosynthesis of SGAs in plants is controlled by enzymes and transcription factors. GAME 9 is a transcription factor that has been investigated in tomato and potato and has been shown to be an important element in the production pathway. In this research, a copy of eggplant’s own GAME 9 transcriptional factor was transformed to the eggplant genome with Agrobacterium-mediated transformation. To this end, the GAME 9 gene was amplified from the eggplant genome and inserted into the pSoup/pGreen0029 vector system. This vector system was inserted into Agrobacterium. Eggplant seedling explants were incubated with transgenic Agrobacterium. The transformation of regenerated plants was confirmed with PCR and efficiency was found to be 1.3%. RNA expression levels were checked by RT-QPCR for 12 confirmed transgenic plants. On the metabolite level, the leaves of transgenic plants were assayed for SGA content using Dragendorff’s reagent method. The transgenic plants’ mRNA and metabolite levels showed plant to plant variation due to the random nature of transgene insertion. Of the 12 transgenic eggplant, nine plants had significantly increased production of both mRNA (at least 2-fold difference) and metabolite levels. In addition, two plants did not show any difference in mRNA level but their SGA amount was significantly increased. The remaining plant had a 0.16-fold decrease in mRNA level but a significantly greater level of SGA than control plants. In the future, these transgenic plants can help illuminate the SGA production pathway of eggplant and be used for the production of economically and medicinally valuable SGAs.Master Thesis Assessment of Liposomal Formulations and Biological Activities of Eggplant Glycoalkaloids(Izmir Institute of Technology, 2019) Tatlıdil, Engin; Frary, AnneBillions of dollars are spent every year in the world for cancer treatments and research. In recent years, bioactive compounds are being tested as promising therapeutics. Among these compounds, eggplant glycoalkaloids: solasonine and solamargine are known to be effective against skin cancer and diseases. However, these compounds are water insoluble. This reduces transdermal drug delivery and the efficacy of solasonine and solamargine. Nanocarriers are used for transdermal drug delivery of water insoluble molecules. In this study, liposomes were used as nanocarriers to increase drug delivery of solasonine and solamargine. In the first stage of the study, empty liposomes produced from four different lecithin types with hydration temperatures of 40°C, 45°C and 50°C were evaluated according to their physical, chemical stability and drug loading capacity criteria at three different storage temperatures (4°C, 25°C, 37°C). The liposome formulation which was most suitable for the continuation of the study was determined. In the second stage of the study, solasonine and solamargine loaded liposomes were produced according to the formulation determined in the first stage and these liposomes were evaluated according to their physical, chemical stability, zeta potentials and drug leakage rate criteria for 3 months and it was determined that the drug loaded formulation was stable during the monitoring process. Furthermore, the release profiles of the drugs in different release media were determined and also the efficacy of the free and encapsulated states of solasonine and solamargine were tested in HaCaT and SCC-25 cell lines and IC50 values were determined.Master Thesis Elecidation of Selenium Tolerance Mechanisms in Puccinellia Distans (jacq.) Parl, Using a Transcriptomic Approach(Izmir Institute of Technology, 2018) Kök, Aysu Başak; Frary, Anne; Eroğlu, SeçkinSelenium (Se) has a versatile chemistry. Therefore, it is present in a wide variety of materials on Earth. Although it is not an essential element for plants, Se provides several survival and ecological advantages. Puccinellia distans (P.distans) is weeping alkali grass which has a relatively fast growth rate and produces a large biomass. It can also hyperaccumulate extreme concentrations of boron and tolerate high levels of salinity. It is known that some plant species can tolerate high concentrations of soil salts and boron while hyperaccumulating Se in their leaves. Therefore, in this study, the Se accumulation and tolerance capacity of P. distans were investigated, and the plant’s Se tolerance mechanism was elucidated using a transcriptomic approach. The results of this study indicated that P. distans accumulated more than 100 mg Se kg-1 in its shoots. Therefore, P. distans was discovered to be a novel Se accumulator plant. Biochemical analyses and RNA sequencing results helped us to decipher the Se tolerance and accumulation mechanism of P. distans. Accordingly, the tolerance mechanism was found to be associated with the upregulation of genes involved in sulfate, selenocompound and antioxidant pathways. Here, we suggest that upregulation of Se assimilation and stress responses genes may have been due to induction of jasmonic acid signaling. In addition, we propose that the cell wall may play an important role in restriction of Se movement to the cytoplasm. Also, we put forward that sequestration of selenate inside the vacuole may be a way that Se accumulates in cells.Master Thesis Molecular Genetic Analyses in Turkish Plum (prunus Cerasifera)(Izmir Institute of Technology, 2018) Çakır, Gülsüm; Frary, AnnePlum is an economically important and popular fruit in Turkey, which ranks in sixth place in world plum production. This fruit is attractive to consumers with its beautiful scent and its delicious taste. In addition, it is an important plant species with its wealthy mineral, vitamin and phytochemical content. The genus Prunus is classified into three groups: the European, the Asian and the American plums. P. cerasifera, which was used in this study, belongs to the European group. P. cerasifera (2n=2x=16) is a Turkish plum drupe species. Since there are many subspecies, it can grow naturally in many parts of Turkey. The genetic diversity and population structure of P. cerasifera have not been studied using molecular techniques. Here, we studied the genetic diversity of 66 P. cerasifera accessions collected from Turkey at the molecular level using 47 sequence related amplified polymorphism (SRAP) primer combinations. The SRAP marker combinations showed reasonable polymorphism. A dendrogram was constructed using the Dice coefficient and unweighted neighbor joining algorithm. The dendrogram revealed three groups and the similarity between accessions ranged from 0.04 to 0.66 with an average dissimilarity of 0.37. Population structure analysis identified three subpopulations (K=3). This is the first genetic diversity analysis of P. cerasifera using SRAP markers. Genetic diversity and population structure data can be useful for determining breeding strategies in P. cerasifera accessions.Master Thesis Characterization of World Spinach Genetic Collection by Using Molecular Markers(Izmir Institute of Technology, 2015) Göktay, Mehmet; Frary, AnneSpinach (Spinacia oleracea L.) belongs to the Amaranthaceae family and is a popular and nutritious vegetable. It is believed that this green leafy plant originated from Persia which is now modern Iran and neighboring countries. In this study we screened 176 spinach world collection germplasm accessions with 15 known SSR markers. The markers produced 58 bands with 57 identified as polymorphic. PIC values of the markers ranged between 0.01 and 0.44. Average PIC value was 0.28. Based on allele analysis with Darwin5 and STRUCTURE tools, 176 individual were clustered into three groups. The first cluster mostly consisted of accessions from Europe and USA and contained 69 samples. The second cluster mostly consisted of lines from Asia and neighboring countries and contained 89 samples. The third cluster did not represent any characteristic according to geographic region, thus it was called an intermixed cluster which contained 18 samples. The maximum genetic dissimilarity of spinach accessions was 0.551 and minimum was 0.019. Average genetic dissimilarity was 0.217. Moreover we sequenced S. oleracea L. cv. Universal nuclear genome via IIIumina MiSeq technology and genome assembly was performed to develop new spinach–specific SSR markers. As a result, 3853 SSRs were identified in the assembled genome and we successfully designed 3275 primer pairs for these identified SSR motifs. These newly developed SSR markers will be helpful to scientists who are interested in spinach genome diversity and breeding.Master Thesis Determination of Genetic Diversity and Population Structure in Faba Bean (vicia Faba L)(Izmir Institute of Technology, 2015) Göl, Şurhan; Frary, AnneFaba bean (Vicia faba L.) is an important legume species because of the high protein and starch content of its seeds. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the symbiotic relationship between the plant and nitrogen fixing bacteria in its roots. Broad bean seeds are consumed as fresh vegetables in many countries throughout the world. However, the genetic diversity found in this germplasm has not yet been characterized and has not been systematically used in broad bean breeding programs. In this project, faba bean individuals obtained from International Center for Agricultural Research in the Dry Areas (ICARDA), Centre for Genetic Resources (CGN), Aegean Agricultural Research Institute (AARI), Nordic Gene Bank (NGB) and Australia (The University of Adelaide, Jeffrey Paull) were examined for their genetic diversity and population structure. For this purpose, 259 faba bean germplasm accessions were characterized using 32 SSR primers. A total of 302 polymorphic SSR fragments were analyzed. According the results, faba bean individuals were divided into two main clusters based on Neighbor-joining algorithm (r = 0.9062) with some clustering based on geographical origin as well as seed size. STRUCTURE 2.2.3 program was used to determine population structure. K was determined as 2 subpopulations. Cluster 1 had 87 individuals; cluster 2 had 162 individuals and 10 individuals were intermixed with results generally agreeing with the dendrogram analysis. A total of 45 well-characterized faba bean individuals were selected for the core collection to be used in breeding studies.
- «
- 1 (current)
- 2
- 3
- »