Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Bacterial Cellulose Production With Gluconoacetobacter Xylinus From Hazelnut Waste(01. Izmir Institute of Technology, 2024) Frary, Anne; Büyükkileci, Ali Oğuz; Frary, Anne; Büyükkileci, Ali Oğuz; 04.03. Department of Molecular Biology and Genetics; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyBakteriyel 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 Population Genomics of Crohn Disease Susceptibility(01. Izmir Institute of Technology, 2024) Sezgin, Efe; Büyükkileci, Ali Oğuz; Sezgin, Efe; Büyükkileci, Ali Oğuz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyCrohn Hastalığı (CD), gastrointestinal sistemin kronik inflamasyonuna neden olan inflamatuar bir bağırsak hastalığıdır. Modern popülasyonlarda CD'ye yatkınlığı artıran genetik yapının, enfeksiyonlara ve patojenlere direnç gibi belirli çevresel stres faktörlerine karşı seçici avantaj sağlayan türetilmiş bir özellik olduğu iddia edilmektedir. Bu nedenle, CD ile ilişkili genlerde seçilim belirtileri olmalıdır. CD riskinin türetilmiş seçilmiş bir özellik olup olmadığını test etmek için, literatür taramaları yoluyla CD ile ilişkili genler ve varyantlar belirlenmiştir. Allen veriseti ve 1000 Genom Projesi aracılığıyla eski ve modern nüfus verileri toplanmıştır. Veriler Plink ve R kullanılarak analiz edilmiştir. 352 CD risk aleli tanımlanmıştır ve CD ile ilişkili alellerin hastalık risk durumu (koruyucu ve duyarlı) atasal ve türetilmiş durumlarıyla karşılaştırılmıştır. Dünya çapındaki dört metapopülasyonun bu alellere göre farklılaşması incelenmiştir. Ayrıca, eski ve modern popülasyonlar arasındaki alel frekansı farklılıkları karşılaştırılmıştır. Günümüz metapopülasyonları arasındaki genetik farklılaşma ve ayrımın, CD ile ilişkili PUS10 ve PPBP_CXCL5 genlerinin etkisine bağlı olduğu, antik ve modern metapopülasyonlardaki ayrımın ise PPP5C, PPBP_CXCL5 ve AIMP1P2 genlerinin etkisi olduğu gözlemlenmiştir. CD prevalansının daha yüksek olduğu popülasyonlarda daha yüksek risk alel frekanslarına sahip olduğu belirlenmiştir. CD ile ilişkili IRGM, OR2B11 ve IL10 genlerindeki varyantlar, atasal ve modern Avrupa popülasyonları karşılaştırıldığında zaman içinde yüksek alel frekansı değişiklikleri göstermiştir. Gen bazlı son seleksiyon analizleri, CD ile ilişkili HERC2, MACROD2, RBFOX1, ITLN1 ve RNFT1P2 genlerinde etkili olan olası pozitif seçilime işaret etmiştir.Master Thesis The Investigation of Intestinal Zinc and Glucose Metabolism Due To Increased Glucose Amount in Obesity(2023) Büyükkileci, Ali Oğuz; Güleç, Şükrü; Güleç, Şükrü; Büyükkileci, Ali Oğuz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyObesity is defined as an excessive accumulation of adipose tissue within the human body. The global prevalence of obesity has seen a marked increase, and our country is no exception to this trend. The pathogenesis of obesity is intricately linked to the consumption of glucose, a phenomenon in which glucose absorption plays a pivotal role via the enterocytes of the intestinal lining. In individuals with obesity, both dietary and blood glucose levels are elevated, thereby intensifying the exposure of enterocyte cells to glucose. This thesis results delved into the interactions between high-glucose-associated zinc metabolism and zinc-dependent glucose metabolism within enterocyte cells. Results revealed a correlation between elevated glucose concentrations and reduced zinc levels within the cells, coupled with the regulation of mRNA levels on zinc transporters. Additionally, observed a reduction in cellular 2-deoxy-glucose uptake upon zinc treatment. Also, indicated that zinc treatments, whether administered to the basolateral or both apical and basolateral sides of the cells, led to the regulation of mRNA levels for glucose transporters, compared to control groups. Remarkably, also observed that specific treatments involving zinc on the polarized sides of Caco-2 cells increased the efflux of glucose from these cells. In conclusion, results suggest that zinc may play a pivotal role in the development of obesity concerning glucose metabolism.Master Thesis Enhancement of Xylanase Activity in Xylooligosaccharide Production From Lignocellulosic Biomass(01. Izmir Institute of Technology, 2023) Büyükkileci, Ali Oğuz; Büyükkileci, Ali Oğuz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyXylo-oligosaccharides (XOS) with prebiotic properties are obtained through xylan hydrolysis. Previously organosolv was found to be an effective pretreatment for XOS production from corncob. However, this process suffered from low XOS yields because of the limited hydrolysis of xylan in the pretreated biomass. This study was designed to test some approaches toward increasing the efficiency of xylanases on the organosolv-treated corncob. The two commercial enzymes (Shearzyme 500L and Veron 191S) used in this study showed a synergistic effect yielding higher XOS compared to single enzyme application. Partial removal of acetyl groups on the xylan in organosolv-treated corncobs enhanced XOS production significantly. The solid loading above 10% decreased XOS yield as it resulted in a highly viscous slurry that may have limited heat and mass transfer. Fed-batch addition of enzyme and biomass did not play a role in the improvement of hydrolysis. In sequential batch mode, the residual enzyme activity from the previous batch could release more XOS from the fresh biomass, though the yield was low. Addition of fresh enzymes to the previous hydrolysate together with biomass provided a more concentrated XOS solution (15.4 g/l) after the second batch. The addition of surfactants into the hydrolysis media to prevent enzyme binding to lignin did not improve XOS production. This study showed that organosolv could be considered an effective treatment for XOS production from corncob and the enzymatic hydrolysis could be improved by optimizing the conditions.Master Thesis Potential of Deep Eutectic Solvent Pretreatment for Xylooligosaccharides Production From Corncob(01. Izmir Institute of Technology, 2023) Büyükkileci, Ali Oğuz; Büyükkileci, Ali Oğuz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyEnzymatic hydrolysis of xylan to produce xylooligosaccharides (XOS) requires pretreatment of the feedstock lignocellulosic biomass. The current pretreatments have some disadvantages, such as the use of harsh chemicals, high energy requirements, and impurity generation. This study aimed to develop a greener method for high-purity XOS production based on mild pretreatment of corncob and subsequent enzymatic hydrolysis. Both deep eutectic solvent (DES) and dilute alkali pretreatments provided approximately 65% lignin removal from the corncob, while 80% of the xylan remained in the solid. When corncob was treated with DES at 130 ○C for 2 h, the total XOS yield in the hydrolysis was 44.1%, and the yield of xylotriose and xylobiose (LDP XOS) was 39.7% based on feedstock xylan. Dilute alkali treatment of corncob at 30 oC for 8 h, provided a total XOS yield and LDP XOS yields of 41.6% and 33.4%, respectively. The enzyme was removed from the XOS solution, while most of the LDP XOS was recovered, using the ultrafiltration system with a 10 kDa membrane. Fermentable sugars were produced from the spent solids as a secondary product using cellulase hydrolysis. This study suggested that DES and dilute alkali-based processes can be considered an eco-friendly approach to XOS production. Since XOS was mostly composed of LDP XOS, they can be preferred as food additives.Master Thesis Screening Spirulina Stranins for Protein Productivity Based on Cultivation Under Photobioreactor Conditionsy(01. Izmir Institute of Technology, 2022) Özkan, Altan; Büyükkileci, Ali Oğuz; Özkan, Altan; Büyükkileci, Ali Oğuz; 03.07. Department of Environmental Engineering; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologySpirulina is an industrially produced algae for consumption as a nutritional supplement owing to its exceptionally high protein content. The delivery of the desired metabolite profiles highly depends on selecting the correct strains for growth. In this regard, the information in the literature is limited as the strains cultivated industrially are unknown, and the strains of academic research were mostly locally isolated or procured from local sources. The current study is the first step of research activities planned to assess the large-scale production potential of Spirulina in Izmir. Thus in this work, Spirulina platensis 2340, Spirulina maxima 84.79, Spirulina platensis 85.79, Spirulina platensis 86.79, and Spirulina platensis 29 were screened for biomass and protein productivity during cultivation under standardized process conditions of a bubble column photobioreactor. The final biomass concentrations were strain specific and ranged from 1.2 to 1.9 g/L. An inverse relationship existed between the logistic model-based final biomass concentrations and the production rate constants. Thus, the peak productivities were more evenly distributed and ranged between 0.15 to 0.20 g/L-day. SP 29 had the ideal protein content vs. cultivation time profile as it was consistently high and varied in the narrow range of 60 to 64%. Higher protein contents could be reached with the other strains, but they also had higher variations during the growth period. The final protein concentrations varied from 0.4 g/L to 1.4 g/L. The highest peak productivity obtained was about 0.11 g/L-day, which could be obtained by three of the strains. The results clearly show the importance of strain selection for sustaining protein-rich biomass production with Spirulina.Master Thesis Effects of Centella Asiatica Saponins on Telomerase Activation and Wound Healing(Izmir Institute of Technology, 2021) Demirbaş, Devran; Büyükkileci, Ali Oğuz; Bedir, Erdal; Bedir, Erdal; Büyükkileci, Ali Oğuz; 03.01. Department of Bioengineering; 01. Izmir Institute of Technology; 03.08. Department of Food Engineering; 03. Faculty of EngineeringCentella asiatica L. is a well-known plant species endemic to Southeast Asia that has noteworthy biological effects. Triterpenoid saponins, comprising more than 80% of the content, are suggested to be the chief compounds responsible for the biological effects. A recent study has described that the extract of Centella asiatica exhibits telomerase activation. In line with these developments, as part of our studies on natural products demonstrating anti-aging properties, we decided to engage Centella asiatica and its components. Within the scope of this thesis, four major compounds, viz. madecassoside, asiaticoside, madecassic acid, and asiatic acid were isolated from the standardized extract of Centella asiatica, and their structures were elucidated by spectroscopic methods. Using in vitro methods, the effects of the extract and purified compounds on cell proliferation under standard culture and oxidative stress (H2O2) conditions, wound healing, and human Telomerase Reverse Transcriptase (hTERT) protein level were investigated. Our experiments were conducted on MRC-5 and HEKn cell lines. It was observed that the standardized extract of Centella asiatica increased the proliferation of the MRC-5 cells meaningfully between 5 to 100 µg/ml. Moreover, the extract showed protective effects on MRC-5 cells at 500 and 1000 ng/ml under oxidative stress conditions. Madecassoside, madecassic acid, asiaticoside, and asiatic acid exhibited the highest proliferative effects on MRC-5 cells at concentrations of 1000 nM (28%), 2 nM (66%), 300 nM (61%), and 300 nM (56%), respectively. Asiatic acid and the extract accelerated cell migration in wound areas that were made on MRC-5 cells up to 32% and 36% in the range of 10 to 300 nM or ng/ml, respectively. The immunoblotting assay studies showed that madecassoside and asiaticoside were increased the expression of hTERT protein level on HEKn cell line by 3.16-fold and 5.62-fold, respectively, at 30 nM concentration. Furthermore, the extract was observed to increase the protein level by 2.62-fold at 300 ng/ml.Master Thesis Succinic Acid Production From Lignocellulosic Biomass by Actinobacillus Succinogenes(01. Izmir Institute of Technology, 2021) Büyükkileci, Ali Oğuz; Büyükkileci, Ali Oğuz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologySuccinic acid is an expensive and high industrial value organic acid that can be used in many industries such as food, cosmetics, chemistry. It can be produced by bacterial fermentation. When cellulose and xylan in the lignocellulosic biomass are hydrolyzed into glucose and xylose with pretreatment process, they can be used as a carbon source in fermentation. This study was designed for the production of succinic acid from pretreated corncob by Actinobacillus succinogenes ATCC-55618. Corncob was pre-treated by organasolv. The cellulose and xylan were hydrolyzed into monomers using commercial enzymes. The optimal enzyme dosages were sought at 50C and pH 5.2, under which conditions pretreated corncob was hydrolyzed for separate hydrolysis and fermentation (SHF). The same test was repeated at 37C and pH 6.8 to find the required enzyme dosages under the simultaneous saccharification and fermentation (SSF). The cellulose and xylan recoveries were 69.2% and 68.8% for SHF, 31.8 % and 41.4 % for SSF. The SHF was conducted using the enzymatic hydrolysate and succinic acid yield was 0.48 g succinic acid/g sugar. In the SSF, the pretreated corncob was used as the carbon source, the succinic acid yields were 0.75 g succinic acid/g sugar. This study shows that corncob treated with organosolv had a potential as carbon source for succinic acid production by A. succinogenes either via SHF or SSF. Although the conditions in the fermentation step were not optimum for the enzyme activity, the SSF was more successful than SHF considering the succinic acid yield on the carbohydrates.Master Thesis Induction of Secondary Metabolism of Some Marine Derived Streptomyces Species, and Isolation and Identification of Their Bioactive Secondary Metabolites(Izmir Institute of Technology, 2020) Gezer, Emre; Büyükkileci, Ali Oğuz; Bedir, Erdal; Gezer, Emre; Bedir, Erdal; Büyükkileci, Ali Oğuz; 03.01. Department of Bioengineering; 01. Izmir Institute of Technology; 03.08. Department of Food Engineering; 03. Faculty of EngineeringSecondary metabolites are natural products with low molecular weight produced by different organisms. These metabolites have a wide variety of bioactivities because of their adaptive roles in the nature. These properties make secondary metabolites important source in drug discovery studies. Streptomyces genus, on the other hand, attracts attention due to their ability to produce many secondary metabolites for the treatment of various diseases, especially infectious diseases and cancer. However, secondary metabolism is not fully expressed under standard laboratory conditions as in nature. This phenomenon limits the discovery of new/novel bioactive molecules from the microbial sources. In this study, a previously studied marine derived actinobacterium, namely Streptomyces cacaoi, was investigated further to discover new antimicrobial metabolites via medium and temperature optimization using Box Behnken design. As a result, GPM medium containing 2.25% glycerol, 1% peptone water, 0.2% CaCO3, 0.1% MgCl2 in distilled water was found to provide the highest chemical diversity with potent bioactivity at 30oC. In subsequent studies, inductive effects of some microorganisms and inorganic compounds on secondary metabolism were also determined. Using optimized conditions, a larger fermentation study was undertaken (25 L) followed by extraction and isolation procedures. Sixteen metabolites were purified by chromatographic methods, and structures of the isolates were elucidated by spectral methods. Thirteen compounds, five of which were new, were members of polyketide-type polyether antibiotics. The structures of other molecules were determined as cyclo(Thr-Trp), 6-hydroxy-6-methyloctanoic acid, and 5-hydroxy-1,6-diazacycloundec-5-en-2-one, and all were found to be new. In antimicrobial tests, most polyethers were found to be active against Gram-positive bacteria. In particular, two new polyethers SC-EG-05 and SC-EG-07 showed higher antimicrobial activity than widely used antibiotic vancomycinMaster Thesis Organosolv Treatment for Prebiotic Oligosaccharide Production From Agro-Food Waste(01. Izmir Institute of Technology, 2020) Büyükkileci, Ali Oğuz; Büyükkileci, Ali Oğuz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyXylooligosaccharides (XOS), which are among the prebiotic carbohydrates, are produced by hydrolysis of xylan in the lignocellulosic agricultural and food wastes. Production processes, such as autohydrolysis and enzymatic hydrolysis following alkali extraction, have some limitations. In this study, it was aimed to develop a process that could overcome those limitations. Corn cob was used as the model biomass and it was pretreated with organosolv. The organosolv pretreatment conditions (solvent concentration, time, temperature, catalyst addition) were adjusted to maximize the lignin removal from the biomass while recovering xylan in the biomass. Delignification could be achieved with 40%-50% lignin removal, and around 85% of the xylan was retained in the biomass. The effect of the organosolv conditions on XOS formation was investigated by the hydrolysis of the pretreated biomass using three commercial xylanases. The organosolv and the enzymatic hydrolysis conditions influenced the XOS formation. The maximum XOS production was observed with the biomass pretreated at 150°C for 1 h with 70% ethanol and 0.1 M MgO. That biomass was enzymatically hydrolyzed at 70°C with 0.6 U/ml xylanase and 70% of the xylan was converted to XOS yielding a hydrolysate containing 9.5 g/l XOS. With the process developed in this study, the need for the application of concentrated alkaline and acidic solutions can be eliminated since the xylan extraction step is not needed. In addition to that, the formation of carbohydrate degradation products can be avoided due to the lower treatment temperatures compared to autohydrolysis. These can simplify the downstream processing following the production of XOS and minimize the environmentally harmful chemical wastes. In this process, a liquid stream rich in lignin and a solid stream rich in cellulose were released. Following a biorefinery concept, these streams can potentially be valorized together with the xylan, so that lignocellulosic wastes can have an added value. This study will be followed by related projects on XOS purification and determination of the prebiotic potential of XOS. In addition to that, the process developed will be tested on other lignocellulosic wastes.