IYTE GCRIS Database (Izmir Institute of Technology)
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Enhancing Wound Regeneration Potential of Fibroblasts Using Ascorbic Acid-Loaded Decellularized Baby Spinach Leaves
No full textDecellularization of plant tissues is an emerging route to fabricate scaffolds for tissue engineering and regenerative medicine. Although significant progress has been made in the field of plant tissue decellularization, functionalization of plant scaffolds is still an emerging field, and loading them with L-ascorbic acid to promote skin regeneration has not yet been reported. L-ascorbic acid is an antioxidant that plays a key role in collagen synthesis as a cofactor of lysyl hydroxylase and prolyl hydroxylase. It has been shown to have significant importance in physiological wound healing by stimulating fibroblasts to produce collagen at both the molecular and the genetic levels. In this work, we aimed to fabricate an ascorbic acid-releasing bioactive scaffold by introducing a stable form of ascorbic acid, L-ascorbic acid 2-phosphate (AA2P), into decellularized baby spinach leaves and investigated its biological activity in vitro. Our results demonstrated that AA2P could be easily introduced into decellularized baby spinach leaf scaffolds and subsequently released within the effective dose range. AA2P-releasing baby spinach leaves were found to increase metabolic activity and enhance collagen synthesis in L929 fibroblasts after 21 days. In conclusion, this study demonstrated the fabrication of a novel functionalized skin tissue engineering scaffold and made a significant contribution to the fields of plant decellularization and skin tissue engineering
Investigation of the Biocompatibility of Various Pulp Capping Materials on Zebrafish Model
No full textTesting the biocompatibility of commercially available dental materials is a major challenge in dental material science. In the present study, the biocompatibility of four commercially available dental materials Mineral Trioxide Aggregate, Biodentine, Harvard BioCal-CAP and Oxford ActiveCal PC was investigated. The biocompatibility analysis was performed on zebrafish embryos and larvae using standard toxicity tests such as survivability and hatching rates. Comparative toxicity analysis of toxicity was performed by measuring apoptosis using acridine orange dye and whole mount immunofluorescence methods on zebrafish larvae exposed to the dental materials at different dilutions. Toxicity analysis showed a significant decrease in survival and hatching rates with increasing concentration of exposed materials. The results of the apoptosis assay with acridine orange showed greater biocompatibility of Biodentine, Oxford ActiveCal PC, Harvard BioCal-CAP and Biodentine compared to MTA, which was concentration dependent. Consequently, this study has shown that showed resin-modified calcium silicates are more biocompatible than traditional calcium silicates
Characteristics of Courtyards of Traditional Houses in Kurtgazi, Birgi
No full textAmaç, geleneksel Kurtgazi evlerindeki avluların özelliklerini anlamak ve koruma sorunlarını tartışmaktır. İçinde yaşanılmaya devam edilen, ulaşılabilir ve özgünlüğünü kısmen korumuş dört avlulu geleneksel ev seçilmiştir. Seçilen avluların nitelikleri yerinde belgelendi, analiz edildi ve değerlendirildi. Avlular doğuda, güneydoğuda veya güneyde konumlanmıştır. Mevcut ve özgün halleri karşılaştırıldığında avlularda toplu eklemeler, çatı yenilemeleri ve zemin kaplama malzemelerinin yenilenmesinin yaygın olduğu ortaya çıktı. Hakim rüzgar yönünün kuzey olması nedeniyle kuzey-güney yönündeki avlu uzunluğunun ilgili avlu duvar yüksekliğine oranı arttıkça doğal havalandırma da artmaktadır. Avlu uzunluğu azaldıkça ve avlu duvarının yüksekliği arttıkça avlunun doğrudan güneş ışığına maruz kalma miktarı azalmaktadır. Güneş ışığından her mevsim faydalanabilmek için bu oranın en az iki olması gerekir. İncir ağacı ve asma gibi yaprak döken bitkiler yazın güneş ışığının avluya ulaşmasını engellerken, kışın güneş ışığının avluya ulaşmasını sağlıyor. Yansıtma yeteneği düşük olan malzemeler özgün haliyle zeminde ve duvarlarda kaplama olarak kullanılmaktadır. Dinlenmek, yemek yemek, hobi yapmak, çamaşır ve bulaşık yıkamak ve kurutmak yılın dört mevsimi yapılan aktiviteler olup, avlularda mevsimlik olarak yiyecek kurutma ve odun kesme aktiviteleri yapılmaktadır.The aim is to understand the characteristics of the courtyards in traditional Kurtgazi houses and discuss their preservation problems. Four traditional houses with courtyards, which are continued to be lived in, accessible and have partially preserved their authenticity were selected. The qualities of the selected courtyards were documented at the site, analyzed and evaluated. Courtyards are positioned at east, southeast or south. Comparison of the current and the authentic states revealed that, mass additions, roof renewals and renewal of ground covering materials in the courtyards were widespread. Natural ventilation increases as the ratio of the courtyard length in the north-south direction to the related courtyard wall height increases since the prevailing wind direction is the north. As the length of a courtyard is decreased and the height of the courtyard wall is increased, the amount of exposition of the courtyard to direct sunlight is decreased. In order to benefit from sunlight in all seasons, this ratio must be at least two. Deciduous plants such as fig trees and vines block the sunlight to reach the courtyard in summers and allow sunlight to reach the courtyard in winters. Materials with a low amount of reflecting capability are used as a covering on the ground and on the walls in the authentic state. Resting, eating, doing hobbies, washing and drying laundry and dishes are the activities in four seasons of the year, and food drying and wood cutting are seasonal activities realized in the courtyards
Lithium: an Energy Transition Element, Its Role in the Future Energy Demand and Carbon Emissions Mitigation Strategy
No full textEnergy transition elements (Li, Ni, Co, Fe, Cu) are gaining importance due to their ability to provide energy and play an important role as primary energy sources. Because of the energy density and power density, Li-ion batteries have the edge over other batteries. Li is distributed in various rock-forming minerals and brines, and geothermal waters. Though lithium-bearing minerals are spread over a broad geographic region, these minerals are confined to certain countries with substantial economic potential. Li is extensively used in batteries, and battery-driven vehicles are growing exponentially to meet the carbon reduction goal of the Paris agreement in 2015 and signed by more than 50 percent of the countries. Nearly 55 million cars supported by Li batteries are expected to roll out by 2030. While this is the demand, its occurrence and concentration/extraction processes are not keeping pace with this demand. The extraction of Li from its ore is an energy-intensive process involving many fossil fuel-based energies. To recover one ton of Li metal, nearly 5 to 6 tons of CO2 is emitted. The CO2 emissions of 28 kWh LFP, NMC, and LMO batteries vary from 5600 to 2705 kg CO2-eq. The end-of-life emissions of an internal combustion engine (ICE) vehicle are 400 kg CO2/vehicle, while Li Battery supports 500 kg/vehicle. The quantity of Li required for a 24 kWh average capacity leaf battery is about 137 g/kWh. While emissions are associated with the manufacturing of the batteries, emissions are also associated with a way that while they are recharged as the recharging source is fossil fuel-based energy. The best option to meet zero net carbon emissions by 2050, as envisaged by International Energy Agency (IEA), is to recover Li from geothermal brines and use geothermal energy for recharging. While hydrothermal energy sources are site-specific, enhanced geothermal system (EGS) based geothermal energy is not site-specific and is found wherever high radiogenic granites are available. High radiogenic granites are widely distributed, and heat recovered from EGS sources can provide clean energy and heat. Extraction of lithium from geothermal waters and using geothermal energy for recharging the batteries will drastically reduce CO2 emissions. It will drive the world towards Net Zero Emissions (NZE) scenario in the future. This is being practiced in Turkey. Future research should develop technology to recover Li from geothermal fluids with low concentration and support EGS development. © 2024 Elsevier Lt
Unraveling the Intriguing Interplay: Exploring the Role of Lncrnas in Caspase-Independent Cell Death
No full textCell death plays a crucial role in various physiological and pathological processes. Until recently, programmed cell death was mainly attributed to caspase-dependent apoptosis. However, emerging evidence suggests that caspase-independent cell death (CICD) mechanisms also contribute significantly to cellular demise. We and others have reported and functionally characterized numerous long noncoding RNAs (lncRNAs) that modulate caspase-dependent apoptotic pathways potentially in a pathway-dependent manner. However, the interplay between lncRNAs and CICD pathways has not been comprehensively documented. One major reason for this is that most CICD pathways have been recently discovered with some being partially characterized at the molecular level. In this review, we discuss the emerging evidence that implicates specific lncRNAs in the regulation and execution of CICD. We summarize the diverse mechanisms through which lncRNAs modulate different forms of CICD, including ferroptosis, necroptosis, cuproptosis, and others. Furthermore, we highlight the intricate regulatory networks involving lncRNAs, protein-coding genes, and signaling pathways that orchestrate CICD in health and disease. Understanding the molecular mechanisms and functional implications of lncRNAs in CICD may unravel novel therapeutic targets and diagnostic tools for various diseases, paving the way for innovative strategies in disease management and personalized medicine
Industrial Symbiosis Model as a Tool of Circular Economy Supported by Lca: a Case Study of Adana Organized Industrial Zone
No full textThis thesis aims to develop an industrial symbiosis model for 24 facilities located in the Adana Organized Industrial Zone (AOSB). Within the framework of the European Union Green Deal (EU Green Deal) and the United Nations (UN) Sustainable Development Goals, which emphasize the global importance of the circular economy (CE) model, this thesis focuses on all aspects of industrial symbiosis to transform organized industrial zones into eco-industrial parks and promote greener and more sustainable production. All facilities have been coded with NACE codes, and potential symbiosis alternatives between them and within in-factory processes have been examined. Potential matches have been identified and evaluated based on criteria such as environmental gains, emission reductions, and decreases in electricity, natural gas, and waste production that could be achieved through symbiosis. Value stream maps have been prepared for all facilities, and tables summarizing production and consumption processes have been created. Potential matches with other facilities have been identified, and a visual network was created through network analysis. Life cycle analyses (LCA) were conducted for two facilities, assessing the potential benefits of symbiosis through LCA. Subsequently, environmental benefits of symbiosis were calculated using emission factors. This study reveals that, as a result of possible industrial symbiosis scenarios, an industrial symbiosis system formed by the companies subject to the thesis could potentially achieve approximately 120,000 tCO2 emission savings and 15,000 MWh electricity savings annually. This study will contribute to future industrial symbiosis efforts in the transformation process of an organized industrial zone into an eco-industrial park.Bu tez, Adana Organize Sanayi Bölgesi (AOSB)' de yer alan 22 firmaya ait 24 tesis için bir endüstriyel simbiyoz modeli oluşturmayı amaçlamaktadır. Avrupa Birliği Yeşil Mutabakatı (AYM) ve Birleşmiş Milletler (BM) Sürdürülebilir Kalkınma Hedefleri kapsamında dünya çapında önemi vurgulanan döngüsel ekonomi (DE) modeli ile organize sanayi bölgelerinin eko-endüstriyel parka dönüşmesi ve daha çevreci ve sürdürülebilir üretimin benimsenmesi amacıyla endüstriyel simbiyoza tüm yönleri ile odaklanmaya çalışan bu tezde tüm tesisler NACE kodları ile kodlanmış ve birbirleri arasında, fabrika içi prosesler arasında olası simbiyoz alternatifleri incelenmiştir. Olası eşleşmeler belirlenmiş ve simbiyoz sayesinde elde edilebilecek çevresel kazanımlar, emisyon azaltımı, elektrik, doğal gaz ve atık üretiminin azalması gibi kriterlerle değerlendirilmiştir. Tüm tesisler için değer akış haritaları hazırlanmış, üretim ve tüketim süreçlerini özetleyen tablolar oluşturulmuştur. Diğer tesislerle olası eşleşmeler belirlenmiş ve ağ analizi yapılarak görsel bir ağ oluşturulmuştur. İki tesis için yaşam döngüsü analizi (LCA) yapılarak, simbiyozun olası kazanımları LCA ile değerlendirilmiştir. Daha sonra, simbiyozun çevresel kazanımları emisyon faktörleri kullanılarak hesaplanmıştır. Olası endüstriyel simbiyoz senaryoları sonucunda bu teze konu olan firmaların oluşturacağı bir endüstriyel simbiyoz sistemi ile yılda yaklaşık 120.000 tCO2 emisyonu ve 15.000 mWs elektrik tasarrufu elde edilebileceğinin olası olduğunu ortaya koyan bu çalışma, bir organize sanayi bölgesinin eko-endüstriyel parka dönüşüm sürecinde bundan sonra gerçekleştirilecek diğer endüstriyel simbiyoz çalışmalarına katkıda bulunacaktır
Explaining Graph Neural Network Predictions for Drug Repurposing
No full textGraph Neural Networks (GNNs) are powerful tools for graph-related tasks, excelling in progressing graph-structured data while maintaining permutation invariance. However, their challenge lies in the obscurity of new node representations, hindering interpretability. This paper introduces a framework addressing this limitation by explaining GNN predictions. The proposed method takes any GNN prediction, for which it returns a concise subgraph as explanation. Utilizing Saliency Maps, an attribution gradient-based technique, we enhance interpretability by assigning importance scores to entities withing the knowledge graph via backpropagation. Evaluated on the Drug Repurposing Knowledge Graph, Graph Attention Network achieved a Hits@5 score of 0.451 and a Hits@10 score of 0.672. GraphSAGE demonstrated notable results with the highest recall rate of 0.992. Our framework underscores GNN efficacy and interpretability, which is crucial in complex scenarios like drug repurposing. Illustrated through an Alzheimer’s disease case study, our approach provides meaningful and comprehensible explanations for GNN predictions. This work contributes to advancing the transparency and utility of GNNs in real-world applications. © 2024 Copyright for this paper by its authors
Investigation of M1a and M6a Rna Methylations in Triple Negative Breast Cancer Cells
No full textMeme kanseri dünya çapında kadınlarda en sık görülen kanser türüdür ve iki alt gruba ayrılır: invaziv lobuler ve invaziv duktal meme kanseri. Bunlardan invaziv duktal meme kanseri, %80 oranında dünya çapındaki meme kanserleri arasında yerini almaktadır. Üçlü negatif meme kanseri ise östrojen reseptörü, progesteron reseptörü ve insan epidermal büyüme faktörü reseptör 2'nin çoğaltılmasını gerçekleştiremeyen agresif bir meme kanseri alt türüdür. Kanser çalışmalarında RNA metilasyonları da hücrenin kaderine etkilerini kanıtlamış önde gelen modifikasyonlardır. Bütün metilasyonlarda olduğu gibi, m6A ve m1A de yazıcı, okuyucu ve silici proteinlerin yardımı ile gerçekleştirilen dinamik bir düzenleme mekanizmasına sahiptir. Bu proteinler, kanser türlerine göre farklı ifadelenme seviyelerine sahiptirler. Bu karakteristik özellikleri ile tedavi ve tespit amaçlı kullanılmaları hedeflenmektedir. Mevcut tez çalışmasında, yazıcı proteinleri olan METTL3 ve TRMT61A proteinlerinin susturulması sonrası, m6A ve m1A metilasyonlarının etkilerinin ve karşılaştırılmasının üçlü negatif meme kanseri hücrelerinden biri olan HCC1143 hücre hattında incelenmesi amaçlanmıştır. Öncelikle, METTL3 susturulması sonrası 72 saatte, maksimum düzey olan %41,2 oranında m6A miktarında azalma gözlenmiştir. Ardından fenotipik etkileri incelemek amaçlı gerçekleştirilen canlılık deneylerinde, METTL3 ve TRMT61A'nın susturulması ile sırasıyla %40,1 ve %27,4 azalma gözlemlendi. Ek olarak, TRMT61A'nın yıkılmasının aksine, yalnızca m6A metilasyonunun azalması sonucu G2/M fazında duraksama gözlenmiştir. m6A miktarının azaltılması sonucu 585 artan/azalan gen ve m1A metilasyonun azaltılması sonucu 687 artan/azalan gen tespit edilmiştir. Bunlardan 151 gen ortak olarak değişkenlik göstermiştir. Gen Ontolojisi zenginleştirme analizleri sonucunda METTL3 yıkımında hücre migrasyonu ve hücre motilite yolakları yoğun olarak gözlenmiştir. m1A azalması sonucu ise bağışıklık sistemi ve canlılığı negatif yönde etkileyen yolaklarda değişkenlik gözlenmiştir.Breast cancer is the most common type of cancer in women worldwide and divided into two sub-groups: invasive lobular and invasive ductal carcinoma. Invasive ductal carcinoma accounts for 80% of breast cancers. Triple negative breast cancer (TNBC) is also an aggressive type of breast cancer that fail to amplify estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2. Intercalarily, RNA methylations have proven their effects on cell fate, especially in cancer studies. m6A and m1A have dynamic regulation mechanisms catalyzed by writer, reader and eraser proteins. These proteins have different expression levels based on cancer types and intended to be used for therapeutic/diagnostic approaches. In the current thesis study, it was aimed to examine the effects and comparison of m6A and m1A methylations in TNBC cell line, HCC1143, after METTL3 or TRMT61A silencing. Firstly, the maximum level of reduction in methylation amounts was attained at 72-hour as 41.2% decrease in m6A amount. To examine the phenotypic effects of silencing, we performed viability experiments and observed 40.1% and 27.4% decrease by METTL3 and TRMT61A knock-down, respectively. Additionally, G2/M phase arrest was observed upon METTL3 silencing. RNA sequencing experiments were conducted to evaluate the effects of knock-down at the molecular level. 585 differentially expressed genes (DEGs) were detected after reduction in m6A and 687 DEGs after TRMT61A silencing. 151 DEGs were common. Based on GO analyses, cell migration pathways were intensely observed in METTL3 while variability was observed in the immune-related and negative regulation of proliferation pathways after TRMT61A knock-down
Bacterial Cellulose Production With Gluconoacetobacter Xylinus From Hazelnut Waste
No full textBakteriyel 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.Bacterial cellulose (BC) is a natural biopolymer with significant potential in areas such as the biomedical, cosmetics, and electronics fields. BC features high surface area, permeability, biodegradability, and modifiability. This study used Gluconacetobacter xylinus to produce BC, optimizing various environmental conditions and media. The focus was on sugars obtained from hazelnut shells pretreated with acid and alkaline solutions. Chemical analysis of hazelnut shells showed lignin, cellulose, and hemicellulose contents of 42.09%, 21.84%, and 22.99%, respectively. Different pretreatments were evaluated for sugar release, with alkaline treatments being more effective. Pretreatment with 1% potassium hydroxide and 3% sodium hydroxide yielded the highest sugar concentrations at 37.8 and 39.0 g/L, respectively. Optimization involved examining inoculation rate, pH, duration, and ethanol presence. The highest BC yield (2369 mg/L) was achieved with 10% inoculation, 10 days, pH 6, and 1% ethanol concentration in the medium. Ethanol addition reduced water retention capacity. FT-IR results confirmed the purity and structural integrity of all samples. This study identified optimal conditions for BC production and demonstrated that hazelnut shells can serve as a sustainable sugar source